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Edit 11/25/2020:
Thanks to a very helpful user (u/slib_) I got more information on cut Marvel characters (Luke Cage, Emma Frost, Mr. Fantastic, Elektra, Cyclops) and was able to update Juggernaut and Jon Talbain’s explanations.
I have plenty of sources to back these claims up, but of course take it with a grain of salt. This comes from official tweets made by Ryota Nittsuma, a Producer of Marvel Vs. Capcom 3. They have been translated by members of the FGC and reported on by multiple news articles. I also talked to some people who have been following Marvel 3 since it was announced, and some who attended its events at Comic-Con.
I got the format and some of the entries of this post from my old account that no longer exists. Although I lost the link to the post.
Both Marvel and Capcom characters are listed, along with the reason they were cut (If any). Bolded characters had significant thought or development put into them before they were removed, while italicized characters had little to no development put into them.

Marvel Characters

• Venom: Marvel didn't want him in the game.
  
• Silver Surfer: Since his board couldn't be incorporated into the engine, he fought without it, but he looked too similar to Iceman.
  
• The Fantastic Four: Capcom wanted to make them all 1 character but Marvel was against it, so they went on to create four separate characters but stopped at Human Torch...
  
• The Thing: Too similar to Hulk.
  
• Human Torch: He was a complete character, but his model and fire VFX took up too much of the game’s memory and was cut. Marvel suggested Super Skrull as a replacement.
  
• Mr. Fantastic: He would have been included since his tech was less painful on the PS360, he's also on one of the games covers, but Marvel said they'd rather have all or none of the F4
  
• Doctor Octopus: Also a complete character, even had a theme. But there were too many glitches with his tentacle attacks.
  
• Miles Morales (Spider-Man): Marvel and Capcom were for it but there wasn’t enough time to begin development. Since he debuted in comics in August 2011, the same year both Marvel 3 and Ultimate Marvel 3 released.
  
• Black Panther: was considered in the Ultimate
  
• Juggernaut: Considered since he had distinguishable qualities from the Hulk. Marvel didn't want him but eventually allowed Capcom to use either Sentinel or Juggernaut, the former was thought to be more iconic to MvC.
  
• Cloak and Dagger: They were liked by the dev team since Cloak (Who would be hovering over Dagger) functioned similarly to Stand abilities in Jojo's Bizarre Adventure. Sadly there was an issue since he visually clashed with the assists. There were also problems mixing two characters into one.
  
• Multiple Man: The game could not handle him multiplying himself.
  
• Rogue: Her personality and the nature of her powers would have conflicted with ESRB. (Y'know, even though we had Morrigan)
  
• Spiral: Took too long to develop due to her 6 arms, multiple swords, and magic attacks
  
• Psylocke: The team liked her and thought to pit her against Strider Hiryu, but she wasn't popular enough.
  
• Spider-Woman: Her origin story and abilities (Flight and electricity) were too similar to Trish.
  

They must've accidentally referenced Ultimate Universe Spider-Woman, where she's a clone of Spider-Man, much like Trish is a clone of Dante's mom. In the prime universe she's her own entity (Albeit with a very confusing history).

• Squirrel Girl: In a meeting, there were more raccoon people in the room than squirrel people, so they chose Rocket Raccoon.
  
• Loki: His personality and abilities weren't viable for a fighting game.
  
• Mystique: Her main gimmick is shapeshifting, and like Loki, not good enough.
  
• Vision: No reason given, just a joke about how overpowered he'd be.
  
• Blade: Deemed too similar to Dante.
  
• Kingpin: Not interesting enough, losing his spot to M.O.D.O.K.
  
• Black Widow: Cut since the game had enough "Gun people".
  
• The Hood: Too many gun people
  
• Captain Marvel: Fun fact: She was known as "Ms. Marvel" at the time, and wore a different black and yellow suit, making it hard to distinguish her from Storm and She-Hulk during gameplay. Pic of her old suit for reference.
  
• Emma Frost: Niitsuma wanted to include her. Shortly after developing her Marvel came to Capcom with the idea of Phoenix transforming into Dark Phoenix on death, which they agreed was better.
  
• War Machine: Supposedly worked on given his name was once listed on the US website.
  
• Elektra: There used to be a Hand Hideout stage, and Capcom at one point said every stage was tied to a character. Given other information she was surely considered.
  
• Cyclops: Marvel said no
  
• Luke Cage (Power Man): Had it not been for the 2011 Tōhoku earthquake and Tsunami and they were able to include the eight extra planned characters for Ultimate, Luke Cage would've been one of them.
  

Capcom Characters

Street Fighter

• Gill: Cut late in development. He had a character model and working moves. Niitsuma said Gill was large and fast making it weird for him to be rendered at the speed Marvel 3 ran at, and they didn't want too many Street Fighter characters. He was replaced by Nemesis, who was just as large but slower making his rendering more appropriate.
  
• Ingrid: Apparently the entire western FGC just hates her for some reason. Niitsuma probably agrees, when asked about her all he said was "You again!?"
  

Darkstalkers
Many Darkstalkers were considered besides the ones listed here.

• Jon Talbain: Had it not been for the 2011 Tōhoku earthquake and Tsunami and they were able to include the eight extra planned characters for Ultimate, there would've been a 4th Darkstalkers rep, and it would've been Jon Talbain
  
• Demitri Maximoff: Midnight Bliss (Presumably his LVL 3) would take too much time to develop and the team feared it'd be controversial.
  

For those who don't know, Midnight Bliss has Demitri turn his victim into a young attractive woman to suit a fetish. Marvel probably didn’t want their characters mocked this way. He also breaths their blood out from their mouth. It take lots of effort to create a new model for each character for one move. To boot there are characters that could not even conceivably be made human, let alone female.

• Anita: An adult Anita was considered and had concept art, but Niitsuma just didn’t like it, saying they went "Too far" and "She's just a kid!"
  
• Donovon: Lost his spot to Hsien-Ko and Felicia.
  

Breath of Fire
The exclusion of many Breath of Fire characters stemmed from western audiences not recognizing them.

• Fou-Lu: A Japan fan-favorite. There were many ideas for him such as his energy sword, monster servants, and shapeshifting dragon form. But that would've taken too much effort.
  
• Nina: She had a character model based off the 1st game and LVL 3 (She summons the other Ninas, like Mega Man's final smash in Smash Ultimate) but she was removed in favor of Firebrand.
  

Like dawg, if they put that much effort in then we could’ve had both...

• Katt: A female staff user was desired, but lost in terms of priority.

Onimusha

• Soki: The team made him an early phase character, but felt he was too weak and slow, and couldn't balance him in time.
  
• Samonosuke: Legal issuesz
  

Red Earth

• Mai-Ling: A female staff user was desired, but lost in terms of priority.
  
• Tessa: She would’ve been paired with rival Doctor Strange, but Niitsuma couldn't convince the team to include her.
  

Other

• Chuck Greene (Dead Rising): Near top of the list too. But didn’t get in.
  
• Franziska von Karma (Phoenix Wright): She was also on the top of the list, but didn’t make it.
  
• Generic Hunter (Monster Hunter): No gender given.
  
• X (Mega Man X): In a similar case to Miles Morales, they wanted him because his adult appearance fit with Marvel characters. But didn't have enough time to develop him.
  
• SonSon (Marvel vs. Capcom 2): A female staff user was desired, but lost in terms of priority. She was also barely recognizable to the western audience
  
• Arieta (Cyberbots): A naked woman piloting a robot might have triggered the ESRB.
  
• Gene (God Hand): lost to Frank West
  

There were over 150 female characters from both sides considered for the game aside from the ones already in.
It's nice to see these unexpected characters at least considered for Marvel vs. Capcom 3. Puts all of the work for even deciding on a roster into perspective. In one of the sources, they said had it not been for the 2011 Tōhoku earthquake and Tsunami, and Marvel rushing them, they would've been able to add eight extra characters. Which of these cut characters would you like to take those spots?

Sources:

Regarding mostly Capcom Characters
Regarding Human Torch and The Thing
Regarding Marvel Characters
More info on Marvel Characters
Regarding Mr. Fantastic and the Fantastic Four
A helpful Reddit comment on Kappa by u/slib_
More information on GameFAQs and NeoGAF, including old tweets can’t cite individually

Pioneers are settlers seeking new horizons and new opportunities in new lands. Pioneer is also a homograph in Lukari, meaning “active, energized, invigorated.”
Both meanings are well-suited for a Lukari scout ship, as the Lukari settle their new colony on Dranuur with their re-united Kentari brethren and as they learn from their Federation allies how to defend themselves with Science!^™ The name also has special affinity with her captain, a Federation Temporal Agent who served on a Pioneer-class vessel.
Meta Analysis
Some people like the bottom line upfront.

• 244K ISA
  
• 433K ISE with a tank
  

Budget: All gear is Mk XV gilded, 1 Lobi ship, five T6 C-store ships, a T6X token, about 100M EC in traits, boff powers, consoles, and doffs. It also requires access to a T5 colony holding (see more at the end). This is not a cheap ship, but neither is it as mind-bogglingly expensive as the highest-end exotic builds, which would at least require another Lockbox ship (Auxiliary Ejection Assembly) and another Lobi ship (Plasma Storm).
Why the Dranuur Scout Ship?
The current sci meta has several different leans and I think emphasizing the Deteriorating Secondary Deflector and Spore-Infused Anomalies is stronger than chasing extra torpedo spreads with the Entwined Tactical Matrices trait and Morphogenic 3-piece set. To that end, I wanted a ship that could strongly emphasize science powers, to the point where I am only using 1 tactical power, 2 engineering powers, and a temporal power. The rest are science. The Dranuur is the best ship at this price point that can support that setup.
I do NOT slot Emitter Synergy nor Checkmate. Emitter Synergy requires Tactical or Intel powers to stack, which this build is extremely short on. Slotting Checkmate would lead down a different offshoot of exotic builds, namely the “clicky” one. Checkmate really benefits from having a Control other than Gravity Well to proc it for more uptime, as does the Unconventional Systems personal trait. If I was going more heavy on Controls or really trying to milk console actives, then slotting Checkmate and Unconventional Systems would bring a large benefit, but at the cost of either a Temporal power or a Secondary Deflector proc.
Other contenders for “best science ship” are all supremely expensive, but I’ll discuss them as well:

• The Verne is regarded as the best science ship, boasting full temporal spec and highly-flexible seating that can stack heavy sci. Its console is also highly-touted. If I was building a Verne, I’d drop Aux to Structural/Emergency Power to Engines and pick up Tactical Team/Engineering Team. This would let me swap out of the Regenerative Crystal Matrix Shield for the Competitive Engines. Engineering Team would be necessary as a low cooldown heal to power Logistical Support. That said, the Verne is an expensive ship and while it has the benefits of full Temporal Spec, its mastery package is inferior to the scout ship (additional 15% CrtD) and it doesn’t have raider flanking. Good time to recall that some Exotics can flank and some don't. For how I like to run my ships, I’d rather have a Dranuur.
  
• The Mirror Crossfield, Glenn, and Edoulg are too tac-heavy for my liking. If you’re using those ships, you’re likely better off pursuing the ETM route with more torpedo spreads and the Morphogenic 3-piece that STO-league.com recommends. The 4 forward weapons on those ships are better-suited for that loadout anyway. The Mirror Crossfield is a Lockbox ship, the Edoulg is a Lobi ship, and the Glenn is a Legendary ship--all expensive.
  

Other alternative ships that aren’t as highly touted but are much cheaper:

• At the C-store level, the Eternal use a similar setup, but it has to drop a science power and pick up an eng. The Fleet Nautilus is better suited to the tac-heavy setup.
  
• The Vulcan T’Pau Scout Ship is slightly inferior to the Dranuur due to lack of temporal seating/worse power bonuses but is very similar. It’s also free assuming you were around during the event. All you have to do is swap CIF for Ionic Turbulence I and Exotic Modulation for Unconventional Tactics on the cheap end or maybe Emitter Synergy.
  

At the end of the day, the Dranuur is the best ship for this type of (tac-light science) build at this price point and I’d say is at least a dark horse contender for best science ship.
Why an Engineer?
The short version is that I didn’t want to spring for another Iktomi on a brand-new toon. Expensive! It’s also satisfying about taking something not as touted and beating the vast majority of those blindly following the meta. The Engineer is the weakest for exotic builds by about 5% final DPS at this level of performance. Tactical captains using exotic builds benefit from Tactical Fleet, Fire On My Mark, and Attack Pattern Alpha (but NOT Go Down Fighting). Science captains benefit from Scattering Field, Science Fleet, and Sensor Scan as well as the utility of Subnucleonic Beam. In contrast, the Engineer has only one useful offensive ability for an exotic build - EPS Power Transfer. Nadion Inversion and Intrusive Energy Redirection are largely wasted on an exotic build (although the latter procs Drain Infection). The Engineering captain’s other abilities are largely focused around durability. The Engineer’s career does add one other niche benefit: the EPS Manifold Efficiency trait. This personal trait allows me to max aux without investing heavily into skills/gear that have Aux power and skipping Emergency Power to Aux. Without the trait, I’m around 127 Aux but that starts forcing me to spec either into skills or specific consoles to keep power levels maxed. Extra +10 power in all other subsystems doesn’t hurt either. The boost does stack if you activate a battery (like the Exotic Particle Flood) as well, but that’s not up all the time like the boost from Emergency Power to Engines is.
I have tried to make up for the lack of offensive captain powers by making it a glass cannon, with only two weak bridge officer heals, plus the captain powers and a couple of personal traits for healing/survivability. Thus, all of the console slots are devoted to offensive purposes (though to be honest, budget serves as a limit here as well, as Plasma Storm or Auxiliary Ejection Assembly are optimal but outside the budget.) Given the results on this ship exceed any other build I've done, I don’t miss the Tac/Sci career powers. If someone wants to expand on this concept using a Tac, be my guest.

Player Information

Player Info	--------------
Captain Name	Laura Jardinero
Captain Faction	Federation
Captain Race	Human
Captain Profession	Engineering
Primary Specialization	Temporal
Secondary Specialization	Strategist
Intended Role	Exotic DPS

Skill Tree

		Engineering		Science		Tactical
Lieutenant		Improved Hull Restoration	Improved Hull Capacity	Shield Restoration	Shield Capacity	Energy Weapon Training	Advanced Projectile Weapon Training
Lieutenant Commander		EPS Flow	Improved Impulse Expertise	Improved Control Expertise	Improved Drain Expertise	Targeting Expertise	Improved Defensive Manuvering
5 Points				Control Amplification	Drain Infection
Commander		Hull Plating		Shield Regeneration		Advanced Weapon Amplification	Improved Weapon specialization'
15 Points
Captain				Advanced Exotic Particle Generator	Advanced Long-Range Targeting	Improved Hull Penetration	Improved Shield Penetration
25 Points
Admiral		Warp Core Potential	Engineering Readiness			Coordination Protocols	Improved Tactical Readiness
35 Points
		Warp Core Efficency				Offensive Coordination
Total of 46 of 46 Points		Engineering Points:	11	Science Points:	15	Tactical Points:	20

Skill Tree Unlocks

Points to unlock	Engineering Unlocks	Science Unlocks	Tactical Unlocks
Unlocks After 2	Training Manual: Emergency Power to Shields III	Training Manual: Engineering Team III	Training Manual: Directed Energy Modulation III
Unlocks After 5	Battery Expertise	Transwarp Cooldown Reductions	Threat Control
Unlocks After 7	Training Manual: Emergency Power to Engines III	Training Manual: Auxiliary Power to the Emergency Batter III	Training Manual: Eject Warp Plasma III
Unlocks After 10	Subsystem Repair	Maximum Shield Capacity	Projectile Critical Chance
Unlocks After 12
Unlocks After 15		Control Resistance	Energy Critical Chance
Unlocks After 17			Training Manual: Aceton Beam III
Unlocks After 20			Defense
--------------	--------------	--------------	--------------

Skill Tree Information

A balanced skill build was chosen to allow maximum selection of relevant science skills while still taking useful weapon skills. Coordination Protocols are an excellent team boost, while Impulse Expertise helps keep the ship in the right spot. Max Weapon Amplification to gain the most benefit from the Imperial Rift 2-piece set.

Build Description

This ship’s primary role is Exotic DPS using bridge officer powers, exotic torpedoes, and other non-weapon effects. The primary offensive statistics for this ship are the Exotic Particle Generators skill (EPG), Critical Chance (CrtH), Critical Severity (CrtD), and Auxiliary power (Aux), +Exotic, Damage Resistance Reduction (DRR), and +Bonus Exotic Damage. Secondary offensive statistics are Control Expertise (CtrlX) and +Projectile Damage as well as Weapon Amplification, since that skill boosts Exotic Critical Severity through use of the Imperial Rift 2-piece.
Research into exotic mechanics has clarified the need and means to balance Aux, Cat1 exotic boosts (including EPG and personal endeavors), Cat2 exotic boosts (including +Bonus Exotic as well as CrtH/CrtD), and DRR effects. When accounting for CrtH/CrtD, this build is within 30% of its Cat1 versus Cat2 exotic boosts including avg Cat1 Preload. The Exotic Calculator for this build is here
This ship used Improved Photonic Officer as its primary cooldown mechanism. Cooldown Reduction Sheet for this build is here

Basic Information	Data
Ship Name	LSS Pioneer
Ship Class	Lukari Dranuur Scout Ship
Starship Beauty shot

Basic Information	Component	Notes
Fore Weapons: 3	Particle Emission Plasma Torpedo Launcher Mk XV	Essential; scales off EPG
	Gravimetric Torpedo Launcher Mk XV	Re-engineer the Epic mod to include [Dmg]. Duration scales off of CtrlX; damage scales off EPG
	Dark Matter Quantum Torpedo Launcher Mk XV	Mostly for the 2-piece.
--------------	--------------	--------------
Aft Weapons: 3	Dyson Proton Weapon Mk XV	Protonic Arsenal 1/3
	Advanced Inhibiting Polaron Turret MK XV	Task Force Ordnances 1/2
	Advanced Inhibiting Chroniton Rapid Mine Launcher	Task Force Ordnances 2/2.
--------------	--------------	--------------
Deflector	Elite Fleet Intervention Protomatter Deflector Array Mk XV	From colony. [ColCrit][EPG][CtrlX][Hullcap][CtrlX/EPG]. Can only have 1 non-Epic EPG mod, but the Crit makes up for it
Secondary Deflector	Deteriorating Secondary Deflector Mk XV [CtrlX/EPG][CtrlX][EPG][ProjDmg][SA +Dmg]	Often the highest source of damage
Impulse Engines	Revolutionary Combat Impulse Engines Mk XV	Imperial Rift 1/2
Warp Core	Revolutionary Warp Core MK XV	Imperial Rift 2/2. This 2-piece is extremely strong and beats the Temporal 2-piece. The 3-piece is a gimmick I didn’t feel like investing in and the colony deflector is stronger anyway. The warp core currently doesn’t gain any mods beyond VR but the loss of [AMP] is more than compensated by the 53% CrtD to all exotics.
Shields	Regenerative Crystal Shield Matrix	Essential due to not slotting Tactical Team - automatically redistributes shields
Devices	Exotic Particle Flood	Essential
	Kobayashi Maru Transponder	Handy little calldown
	Deuterium Surplus	Extra speed boost in a pinch
--------------	--------------	--------------
Engineering Consoles: 3	Temporal Vortex Probe	From this year’s anniversary probe. Clicky is good for about 5K.
	Hull Image Refractors	+20% damage and a bunch of temporary hull is quite good for a universal console. Exchange purchase.
	Neutronic Eddy Generator	Very high damage, has to be used at the right time or else you will toss enemies everywhere and tick off your teammates
--------------	--------------	--------------
Science Consoles: 5	Restorative Particle Focuser Mk XV [EPG][CtrlX]
	Restorative Particle Focuser Mk XV [EPG][CtrlX]
	Exotic Particle Focuser Mk XV [EPG][CtrlX]
	Exotic Particle Focuser Mk XV [EPG][CtrlX]
	Exotic Particle Focuser Mk XV [EPG][CtrlX]
--------------	--------------	--------------
Tactical Consoles: 3	Lorca’s Custom Fire Controls	Lorca’s Ambition 2/2, essential
	Constriction Anchor	Exchange purchase; great passive, weak active
	Delphic Tear Generator	Exchange purchase; great passive, decent active
--------------	--------------	--------------
Universal Consoles: 1	Temporal Disentanglement Suite	One of the better crit consoles at this price point. I could have added another focuser, but more crit is helpful.
--------------	--------------	--------------

Officers and Crew

Bridge Officer Information	Power	Notes
Officer 1: Lt. Commander (Universal - Science)	Subspace Vortex III	Exchange purchase, but really worth it
Trait: Restorative Protomatter Specialist, Leadership, & Efficient	Photonic Officer I	Cooldown mechanic, triggers Improved Photonic Officer
	Hazard Emitters I	Cleanse/Heal
Officer 2: Lieutenant (Universal - Engineering )	Auxiliary to Structural I
Trait: --	Emergency Power to Engines I	Essential. This does a couple of things--one, allows me to reset Evasive Maneuvers with a doff. Two, triggers EPS power transfer to max out Aux.
Officer 3: Lt. Commander (Universal - Science/Temporal)	Tyken’s Rift II	AoE Secondary Def proc. Off-cycle from Gravity Well
Trait: Leadership/Space Warfare Specialist	Chronometric Inversion Field I	Procs Exotic Modulation, also a source for Spore-Infused Anomalies. Helps reduce incoming damage.
	Very Cold In Space I	Winter Event Store
Officer 4: Commander ( Sci )	Gravity Well III
Trait: Efficient & Pirate	Destabilizing Resonance Beam II	Excellent SecDef proc
	Delayed Overload Cascade II	Giant damage potential, works great on clumped enemies but will scatter them so must be timed well
	Structural Analysis I	Excellent AOE Officer
Officer 5: Ensign ( Tactical )	Torpedo Spread I I	Preferably the Gravimetric torp
Trait: Superior Romulan Operative

Duty Officer Information	Power	Notes
1	Conn Officer	Recharge Evasive Maneuvers after Emergency Power to Engines
2	Security Officer	26 of 47; % to boost DoT on use of Tac powers; % to boost Crit on use of Temporal powers
3	Security Officer	32 of 47; CrtD from Science abilities, Exotic damage boost from Intel (can't use the latter)
4	Projectile Weapons Officer	Chance to boost CrtD on firing projectiles; Rare
5	Matter-Anti-Matter Specialist	Chance for Gravity Well to knock Engines offline
6	Gravimetric Scientist	Change to create aftershock Gravity Well

Traits

Personal Space Traits	Description	Notes
Context is for Kings	Each second while in combat, if you did not take damage in the past second, you gain a damage bonus. Otherwise, you gain a boost to your Damage Resistence Rating. Each second while in combat: If you did take damage in the past second: +3 All Damage Resistance Rating for 10 sec If you did not take damage in the past second: +1% Bonus All Damage for 10 sec	Exchange purchase; replace with Innocuous if budget limits
Fleet Coordinator	+2% All Damage per Team member (Self included), up to 10%
Enlightened	+15% Hull Regen and 15% Exotic Damage	Exchange purchase
Give Your All	Activating any Engineering Bridge Officer Ability will grant you additional damage reduction for a short time. This will register as a portion of the damage being Dodged. On activation of Engineering Bridge Officer ability: Reduce incoming damage by 20% for 3 sec	This ship cycles engineering powers frequently; Engineering R&D
Grace Under Fire	If you take more than 20% of your hitpoints in damage within a 5 second period, the cooldown on Miraculous Repairs is reset. This trait will only trigger when Miraculous Repairs is already on cooldown, and can only trigger once every 90 seconds.	Eng career
Ablative Shell	After receiving a total of 10,000 Damage (pre-resist), trigger Ablative Shell: +X Hit Points every 0.5 sec for 3 sec, +33 All Damage Resistance Rating for 3 sec, May only trigger once per 30 sec	Excellent defensive trait
Particle Manipulator	Gain .2% Critical Chance and .1% Critical Severity for Exotic Damage abilities, per point you have in the Starship Exotic Particle Generator skill. The Critical Chance bonus gained from this Trait is capped at +50% (attained by having 250 Particle Generators skill), but there is no cap on the Critical Severity bonus	ESSENTIAL; Science R&D
EPS Manifold Efficiency	Boosts all power levels on use of Emergency Power to Engines and batteries.	Eng career
Resonating payload Modification	Torpedo weapons apply -5 Kinetic and Physical Damage Resistance Rating for 10s (max 10 stacks)	Exchange purchase

Space Reputation Traits	Description	Obtained from
Auxiliary Power Configuration - Offense	+6.25 Bonus All Damage, +6.25 Accuracy	T4 Nukara
Particle Generator Amplifier	5% Bonus Exotic Damage	T2 Iconian
Advanced Targeting Systems	+16% Critical Severity	T2 Dyson
Precision	+4% Critical Hit Chance	T2 Romulan
Chrono-Capacitor Array	9.4% Bridge Officer Recharge Haste	T2 Temporal

Starship Traits	Description	Notes
Improved Photonic Officer	Extends Photonic Officer duration by 10 seconds. When activating Photonic Officer, +25% bonus shield healing, exotic damage, and hull healing for 30 seconds	Essential, but pricy. From Tholian Iktomi (Lobi ship)
Improved Gravity Well	Duration of Gravity Well increased from 20 sec to 40 sec Recharge time of Gravity Well reduced by 20 sec Primary Target of Gravity Well suffers -20 All Damage Resistance Rating for 40 sec	Longer Grav Wells amplify all the other AOEs. Great trait.
Strike From Shadows	When damaging a foe that doesn't have you targeted, for 30 seconds: decrease threat generation, +5% CrtH and +5% bonus All Damage. Also placate the target	Damage and threat reduction
Ceaseless Momentum	Whe firing torpedoes, +5% bonus kinetic damage for 45 seconds, +5 bonus kinetic damage resistance rating for 45 seconds, -1 sec to recharge time of torpedoes	This is the one cheap trait on this toon (for Feds)
Exotic Modulation	While this trait is slotted, using Directed Energy Modulation or any Temporal Operative ability will provide a large boost to Exotic Damage for a short time.	Procced by CIF
Spore-Infused Anomalies	While this trait is slotted, using any science or intel ability causes anomalies to do extra damage.	Second-or-third-highest damage source; Somerville Intel Science Ship

Other Information

Subsystem Power Settings	Value (Target/Display)	Notes
Weapons	30 / 79
Shields	35 / 56
Engines	35 / 66	Could set this higher to gain an AMP stack if the Warp Core gets [AMP] added to it.
Auxiliary	100 / 130

Set Name	Set parts: # of #	Effects	Notes
House Mo’Kai science	Imperial Rift 2/2	Boosts Exotic CrtD by 55.9% (scaling off Starship Weapon Amplification skill, which is at 105 on this toon)	Essential
War Discretion	Lorca’s Ambition 2/3	Stacking CrtD bonus
Arsenal Synergy	Protonic Arsenal 2/3	3% CrtH and 23% Photon Torpedo Weapon damage	Essential
Task Force Tunings	Task Force Ordnances 2/3	Boosts Chroniton and Polaron damage, adds turn rate	Weak but low opportunity cost. See below.

Ship Stats	Value	Notes
Hull	61785
Shields	17432
Global Critical Chance	30.4%	Resting; Particle Manipulator adds 50%
Global Critical Severity	150%	Resting; Particle Manipulator adds 39.5%
EPG	395	Resting; spikes at 520
CtrlX	300	Resting
Turn Rate	55.6 deg/sec	Resting + EPtE
Flight Speed	83.30	Resting + EPtE

Further Commentary

Controls and keybinds
With as many abilities and synergizing concepts as this ship employs, an efficient control scheme is essential. There are many ways to set up such a ship, so I don't pretend to assume that my way is superior. It works for me, especially with my background in RTS and MOBA games, where pushing many different keys quickly is essential:

• [Spacebar] is my spambar. It includes Auxiliary to Structural, Torpedo Spread, Photonic Officer, Sensor Analysis, and Emergency Power to Engines, Structural Analysis. I tossed Constriction Anchor here as well and Subsystem Targeting - Shields here as well mostly so I wouldn’t forget to use them.
  
• [2] is my big buff key. It includes EPS Power Transfer, Diversionary Tactics, Nadion Inversion, Intrusive Energy Redirection, Exotic Particle Floods, Engineering Fleet, Kobayashi Maru Transponder
  
• [3] is my bread-and-butter Exotic combo: Gravity Well, Subspace Vortex, DRB, and Tyken's Rift, Very Cold in Space, Chronometric Inversion Field. I have to not spam this too hard for fear of reactivating Subspace Vortex
  
• [4] are my basic heals: Hazard Emitters, Brace for Impact, Rotate Shield Frequency, and also Auxiliary to Structural.
  

I also bind "Fire all weapons" to right mouse.
Everything else is manually triggered. Notably, Delayed Overload Cascade should only be triggered in specific situations (see below).
ISA/ISE Piloting Tips
Pre-buff the spambar prior to countdown (in PUGs) or prior to launch call (premade). Hit the first group with basic Exotic combo, leading with GW. On ISE, use Temporal Vortex Probe and Delphic Tear and big buffs here as well. Next, hit Evasive Maneuvers and fly to the left side, using any remaining big buffs. Target the generator with Tyken's Rift and whatever other exotic powers are available along with another torpedo spread. Save GW/SSV. As the generator is about to die, turn and engage the ball of Nanite Spheres with a second Grav Well, SSV, and any remaining console actives (NOT Neutronic Eddy) + torpedoes. Can use a Reinforcements cooldown here as well.
Activate Evasive Maneuvers and fly to the right side, rinse and repeat with as with the left. Save big active heals for this part because PUG teams don't always fly over to right generator quickly. As it's dying, turn back on the gateway. Activate Quantum Singularity Manipulation and FIRE EVERYTHING! Close to 5 km and drop the Anti-time bubble and GW with the boost from Quantum Singularity Manipulation. Since this ship can flank, flanking angles on cubes, transformers, and generators are important. With any luck, the 425 CtrlX Grav Well will also suck in the remaining spheres. THIS is where you use Neutronic Eddy Generator to avoid flinging spheres all over the map. Finish off the tac cube (Delphic and Temporal Vortex Probe should be up again) and that should be it. On a slower run, I can often get a second round of big buffs and console actives on the gate or tac cube.
Piloting videos
I recommend this video because e30rnest is an excellent pilot and teacher.
Personally, here’s video of my record run (on ISE). If there’s interest, I might make a video with commentary.
When to fire things that toss enemies
You can easily anger your allies on most TFOs by hurling enemies vast distances with effects like Delayed Overload Cascade or Neutronic Eddy Generator instead of killing them. I have found that the best time to use these is on large, stationary targets with large numbers of small enemies clustered around them that are almost dead. Basically, GW the thing you want to kill, wait until the small targets are pulled in close and are low, and THEN trigger your Neutronic Eddy and/or DOC.
Budget considerations
I do not see how the core of this build can be easily cheapened without seriously degrading performance. The Starship traits on this build come from a Lobi ship and 4 C-store ships, plus a T6X token. It took a combination of grinding and some monetary investment to make this build happen, plus buying on sale. Improved Photonic Officer is good enough that I was willing to grind the Exchange for 4 months to pick up the ship/trait, BUT if that's too much to ask, I completely understand. You can still make this build work by dropping the Chrono Capacitor Array reputation trait and using Torpedo Astrometric Synergy instead; but there will be other cooldown issues (chiefly in Eng and Tac). If I was trying to save money, I would drop Exotic Modulation and Strike From Shadows first and replace with Improved Critical Systems or Unconventional Systems.
However, if budget was truly limiting, here's what you need to set up a properly successful EPG build in this particular subflavor:

• Gravity Well III
  
• The three SecDef procs: Tyken's Rift, Destabilizing Resonance Beam, and Structural Analysis
  
• Gravimetric and Particle Emission Plasma Torpedo Launchers with Projectile Weapons Officers to reduce reloads
  
• Constriction Anchor and Delphic Tear consoles (these will require some EC farming)
  
• Lorca’s Ambition console + torpedo (Discovery rep)
  
• Emergency Power to Engines I with Emergency Conn Hologram doff (VR reward from Phoenix Box)
  
• Subspace Vortex III, Very Cold in Space, and Delayed Overload Cascade if you’re running a ship that can do it. This requires some EC farming If I had to drop a sci power, I’d drop DOC first.
  
• Deteriorating Secondary Deflector Mk XV (the most important piece)
  
• Temporal Defensive Initiative Starship Technologies 2-piece set if Imperial Rift 2-piece is not available
  
• Temporal Operative specialization
  
• Particle Manipulator (Science R&D, possibly the second most important piece)
  
• Fleet Coordinator (always slot this)
  
• As many Particle Focusers with [EPG][CtrlX] as you can slot from the research lab
  
• Exotic Particle Flood devices and Quantum Singularity Manipulation active.
  

The above core build will still cost around 30M give or take and several pieces of reputation gear, but is much more attainable. Mark does not matter much for most items, but definitely get the Deteriorating Secondary Deflector to Mk XV.
Acquiring the Dranuur
Since this ship requires a T5 Colony to acquire, it can be difficult to buy despite technically being cheap/free with T6 reputations. My personal recommendation is either asking in the NoP Public Service channel or making a reddit post on /sto asking for a fleet invite, which is how I got mine. Note that you will need to be IN the fleet and not just on the map to buy the ship.
What is that Weapons Layout? I mean, MINES?!
The cheesy answer is that, aside from the Gravimetric and Particle Emission Plasma Torpedoes, weapons on a science ship are there to complete set bonuses, so why not have some fun with it? I have 3 torpedo launchers, a cannon turret, a beam array (sort of), and a mine launcher. A little bit of everything!
Now to the serious answer. For set bonuses, the Protonic Arsenal 2-piece brings excellent crit, so that’s a no-brainer to slot the Proton Weapon. Same with the Dark Matter Torpedo combined with its console. The Advanced Inhibiting Weapon has a guaranteed -10 damage resistance rating effect on any target slower than you--basically all the important ones. Lastly, the mine launcher provides a fairly weak set bonus, but the weapon does fire, it launches mines ahead of the ship rather than behind like most mines, and it is amplified by Ceaseless Momentum, so it does pretty well for an afterthought weapon.
Concluding Remarks
I've pushed this build farther than I'd ever thought I would personally achieve and it is not quite my most expensive but certainly up there. While there is certainly room for me to grow as a pilot, I am not pursuing major gear upgrades. This is the end result of the ongoing exploration that tilorfire27 and I have been doing into exotics and I am darn well-pleased with it.