Netherrealm games often base their roster around the game's plot. (though not always, as seen with the Joker's inclusion in Injustice 2 - he only appears in the story mode once as a hallucination, and he's long dead by the events of the game, but you've gotta have the Joker) I'd rather avoid the "superhero civil war" trope, as Injustice already covered that pretty thoroughly, but there'd need to be a reason for the heroes to fight each other.
What I came up with is that Doctor Doom and Kang the Conqueror are having a war through time travel, which is shattering the space-time continuum. This leads to versions of heroes from different points in time (times that they'd rather forget) or alternate universes showing up in the main universe. (it also serves as a justification for mirror matches) Obviously, this would mean that
Doctor Doom (1) and
Kang the Conqueror (2) would be playable.
With Doom and Kang in here, we'd need to have the teams that are most famous for opposing them.
The Fantastic Four
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Mr. Fantastic (3) - he's Doom's arch-enemy, and he's distantly related to Kang; he kind of has to be in here. (plus, the Council of Reeds would provide a ton of different options for alternate costumes)
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The Thing (4) - the ever-lovin' blue-eyed Thing ain't about to miss a chance to smack Doom around!
While I could have included Sue and Johnny, I feel like it's going to be tough enough to fit everyone in here as it is. (maybe they'd be free DLC, or the first characters revealed for a season pass)
The Avengers
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Iron Man (5)
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Captain America (6)
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Thor (7) - all three of these are mainstays of the Avengers since the silver age, and they feel like they have to be in here
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Black Panther (8) - he makes for a nice contrast with Doom, and he has history with the Fantastic Four
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Captain Marvel (9)
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The Vision (10)
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Scarlet Witch (11) - all three are regular members of the Avengers, popular characters in their own right, and have plenty of opportunities for evil alternate versions of themselves
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Ant-Man (12) - specifically the Hank Pym version, though Scott Lang could be a premiere costume like Bizarro in Injustice. Hank's own worst enemy is himself, in more ways than one, and having him beat up his Ultimate version or a version who stayed as Yellowjacket in story mode could be cathartic
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The Wasp (13) - I feel like Ant-Man and the Wasp are severely under-used compared to the other founding Avengers. To differentiate her from Hank, she could focus on shrinking and flying, while Hank could have a moveset inspired by his Dr. Pym: Scientific Adventurer phase where he grows or shrinks various objects to use as weapons, in addition to his growth powers
I originally had She-Hulk and Hawkeye in here, mostly for the interactions (and in Hawkeye's case, having a version of him
mention the Justice League in a mirror match - Netherrealm is owned by WB, to my knowledge, so I think they could get away with that), but I felt like I was overdoing it with Avengers members, so I cut them.
There are heroes who feel like they have to be in here, like
the Hulk (14) or
Spider-Man (15). I don't think I need to explain why they're being included - even if they don't have much in the way of ties to either villain, you'd have to be crazy to make a Marvel crossover without these two.
However, every single character that I've mentioned so far was made in the 60's; I figure it's time to get some newer characters in this.
Ultimate Spider-Man (16) (Miles Morales) and
Ms. Marvel (17) (Kamala Khan) are easily Marvel's biggest success stories of the 2000s; I'm sure some people might find issues with there being two Spider-Men, but they've been differentiated enough in other games, with Peter being more tech-focused and Miles having his stealth and venom blast.
Marvel's got at least one other major earthbound super-team that should be included in here -
the Great Lakes Avengers the X-Men!
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Wolverine (18) - it would be more shocking if he wasn't in here.
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Storm (19) - aside from being one of the more popular X-Men, I could see there being fun with alternate timelines where she never met Professor X or she let the fact that she was worshipped as a goddess go to her head
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Rogue (20) - she's connected to Captain Marvel and a character that I'll mention later, and she was previously evil, so an easy alternate timeline is one where she stayed that way. Plus, I could see her having a unique action (like what Injustice characters have) where she pulls off her glove, grabs someone, and if it connects, her unique action is replaced with one of the opponent's powers/skills
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Magik (21) - I think her powers (summoning demons, the Soulsword, the Stepping Discs) would work well for a fighting game, and it would be pretty easy to make an evil alternate version of her
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Cable (22) - the heroes need a time traveler of their own to take the fight to Kang and/or Doom; I debated between him and Dr. Strange, but I figured I'd keep the focus on the Fantastic Four, Avengers, and X-Men.
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Deadpool (23) - he seems like some much-needed comedic relief, especially with She-Hulk and Hawkeye cut
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Magneto (24) - he'd be firmly on the side of the X-Men, though some of his time-displaced versions could be from the points in time where he was villainous. (if possible, I'd love for there to be a
"Welcome to die!" reference in a mirror match)
While he doesn't seem to be affiliated with any of the other characters (though he was on the West Coast Avengers once), I'd like to include
Moon Knight (25) in here - with this game involving time travel, it could be neat to have various versions of Moon Knight in different time periods, since the role is inherited. (there was an issue where Kang fought different incarnations of Moon Knight throughout history, and both Kang and Moon Knight are tied to ancient Egypt)
The roster needs more villains than just Doom and Kang. We've got a Fantastic Four villain and an Avengers villain, so I feel like it's time to include some X-Men villains.
Apocalypse (26) has a versatile power-set, and he could serve as a rival for Kang in ancient Egypt, along with a threat in his own right. (and he's got a long, confusing history with Cable) Plus,
he'd have some great dialogue.
I think that
Mystique (27) would work well as a villainous wildcard, with it never being clear who's side she's on. Plus, she's a shapeshifter, so there could be some fun with that, and she's got ties to Captain Marvel (seeing as she's Carol's former arch-enemy) and Rogue (since she's Rogue's adoptive mother).
I'd like to include a Spider-Man villain, since outside of Venom, Marvel vs. Capcom doesn't really use them. Doctor Octopus seems like a natural inclusion, though the concept of someone who can grapple you from across the screen seems like a balancing nightmare. I'll go with
Green Goblin (28), who seems like he'd have a lot to work with between his pumpkin bombs, glider, and the fact that he's basically a super soldier.
While I could stop things here, there's one more character that I'd want to include, since most of his "family" is in the roster -
Ultron (29). Aside from being one of the main Avengers villains, and having ties to Ant-Man, the Wasp, Scarlet Witch, and the Vision, a version of him could be reprogrammed by Kang or Doom to serve as a recurring villain along with Doombots and Kang's similar robotic duplicates.
There are SO many other characters that I wanted to include - aside from She-Hulk and Hawkeye, there's Taskmaster, Namor, Cyclops, Phoenix, Doctor Strange, Squirrel Girl, America Chavez, Shuma-Gorath... I could be here all day, but thirty already felt like it was too much for a base roster for the first game in a series.
