JesseNeon

Frankly, here's how I see it:
M:UA2: Civil War will probably have around 32 characters.
My guesses:

Pro-Registration:
Iron Man (No doubts about this guy. He might not be playable, though. They could make Iron Man and Cap unuseable)
Venom (Already in M:UA AND a member of the Thunderbolts)
Song Bird (Thunderbolt)
Swordsman (Thunderbolt)
Mach IV (Thunderbolt)
Doctor Octopus (Hey, he was a thunderbolt, AND had a Spider-man movie. You never know with Marvel.)
Penance/Speedball (Not sure about him. Maybe.)
Moonstone (Thunderbolt)
Mister Fantastic (Definitely.)
Yellowjacket (Maybe. His powers would be tricky.)
Bishop (Already in a marvel game AND in the CW? He'll be here.)
Deadpool (Same as Bishop)
Captain Marvel
Nighthawk (Possible)
She-Hulk (Probable)
Ares (Probably. I think so, at least)
Black Widow (Already in M:UA, so probably)
Ms. Marvel (Same)
Sentry (Marvel's superman. Maybe?)
Wonder Man (...We'll see)
Morbius (It would be cool, admit it.)
Scorpion (The girl)
Radioactve Man (Gotta be. He's a main T-bolt, and was in M:UA)
Task Master (Probably not, but it would be sweet)
Blade (Marvel stuck him on the pro-reg side on their website. I don't remember seeing blade in the CW, but they MIGHT just want to tie that loophole up once the came comes through)


Anti registration:
Captain America (R.I.P. And duh)
Archangel (Possibly)
Black Panther (Another M:UA return)
Cable (Hey, Deadpools here, Cable will be too.)
Daredevil (M:UA return)
Cloak and Dagger (They were key to the Civil War)
Hercules (Come on, he smashed robothor's brains all over the Baxter Building sidewalk. He's GOTTA be there.)
Human Torch
Invisible Woman
Punisher (Maybe)
Like Cage (All these guys are M:UA returns, minues Iron Fist and Ronin)
Doc Strange
Iron Fist
Ronin
Wolverine
Spider-man
Spider Woman

Also:
We know that the hulk will be in the game, even though he was on a different planet during the Civil War. That's okay, it doesn't have to make sense. Marvel has already stated that the games are in a different dimension, so we don't have to understand. I immagine most of the movie-made heroes will be here, Elektra, Ghost Rider, Silver Surfer, and so on even though they didn't show during the war.

Others:

I think the Young Avengers might make an appearance. Possibly the Runaways as well. I'm not sure how many X-men will show, since most stayed out of the conflict, but knowing Marvel, they'll probably use Storm, Nightcrawler, Colossus, Cyclops, Beast, Gambit, and a few others. I wouldn't be surprised to see more villains in the pro-reg side, due to the thunderbolts army, nor would I be surprised to see random characters thrown in just because they're popular. Example: Anita Blake? Maybe? We'll see.