A reminder of who is in the cinematic universe (no TV/netflix here folks) -
The Good - Iron Man, Captain America, Hulk, Thor, Black Widow, Hawkeye, Scarlett Witch, Quicksilver , Vision, War Machine, Ant-man, Spider-Man, Black Panther, Starlord, Groot, Rocket , Gamora , Drax, Howard the Duck , Dr Strange,
coming soon - Wasp, Captain Marvel , Nova ?
The Bad - Iron Monger, Whiplash , Killian, Red Skull, Winter Soldier, Zemo, Abomination, Loki, Malekith, Destroyer, Ultron, Strucker , Ronan, Thanos, Nebula , Collector,Kaecilius, Dormamu
coming soon - ???? Vulture ?
That's already possibly 42 characters to choose from. There are some redundant characters though , like Hulk will get in over abomination and I doubt they'd put in war Machine either. I'd also figure if Rocket came in , Groot would just be part of his character select , Gamora and Drax are probably out. Wasp/ant man would be the same character and I doubt either would make it in , too one note. Would make a better assist. I only wrote down Howard as a joke and Captain Marvel / Nova are also pretty similar aren't they ? Quicksilver is uh.. you know .. in the movies so that means Scarlett Witch would probably make it in but she'd have to be her movie version for sure , no potential confusion with the Xmen stuff (which also has the better movie Quicksilver...) Hawkeye is kind of lame and unpopular but black widow might work. So basically narrowing out the rest you still have at least 12 solid good guy Marvel characters only from the movies.
The movie villains are largely lame so it's pretty much down to picking the best of the worst - Ronan, Whiplash , Destroyer , Loki , Thanos , Dormamu , Red Skull, Winter Soldier would probably all work. That means you'd need to pull 4 bad guys from the comics to even out the roster to 12 bads for 12 goods , or cut it down to 8 and 8. My money is on 8/8 because if it's also 8/8 on the capcom side you'd end up with a nice 32 characters to start with which is roughly where MVC3 launched. Given that - reducing my selected 12 down to 8 , well, I guess I'd still throw captain America, Iron Man, Hulk and Spider-man in there because they've been in a bunch of the VS series already. For the other 4 - I think I'd keep the Rocket/groot dual character and Black Panther (easy wolverine replacement) , Scarlett witch just to make sure a woman is in there (and they could make her play similar to storm) and Doctor Strange because his movie just came out and he's so hot right now. I guess a single substitute is that maybe Thanos would be the main end boss and Nebula is on the bad team.
As for the Capcom side , well I don't know Ryu/Bison is the obvious SF2 rep Rashid/Necalli as the recent SF rep. Then I guess Morrigan because of course and uh maybe throw Dmitri in there (complete with fully functioning midnight bliss special attack). Then Dante/Virgil repping DMC and uh Megaman X finally repping megaman but in a twist throw Dr. wily in there complete with UFO and an attack that sends met hats out as projectiles. Chris/Wesker could return to rep resident evil. The last 4 could really be a mix of whatever - Frank West , Phoenix wright, Sir Arthur /Red Aramar , bionic commando , that monster hunter cat thing .