Mega Man X
In every vs. Capcom game we've had some form of Mega Man, but never the best one. X is the older darker version of Mega Man. The Tim Burton Batman to the Adam West Batman. The Bomberman Zero of Bomberman... well actually that example sucks. Anyway X has all the abilities of other versions of Mega Man, but if you met the right conditions in his games you could unlock Ryu's moves. Sounds like a good idea for Ultras to me.
Zero
After already appearing in Tatsunoko vs. Capcom and being the coolest character in the game it seems silly to not put him in. Zero is fast, has tons of power, and has a look to him that is the perfect combination of awesome and retarded, which to me is necessary in a vs. game.
Blade Master Alastor
Viewtiful Joe was alright in Tatsunoko vs. Capcom, but part of the appeal to the vs. series is not just getting the Ryus, and Chris Redfields, but also getting the side Characters. Blade Master Alastor was the rival character in Viewtiful Joe. He has all kinds of crazy sword and lighting powers, and he would be a nice cult favorite character to throw in.
Monster Hunter Guy
As one of the most popular franchises in all of Japan it's time Capcom milks this property in their fighting games. The Monster Hunter himself is pretty hardcore. He goes out and kills dinosaurs, and when he's done he turns them into clothes and weapons and then goes out and kills more dinosaurs to create more shit. Somehow this has to be made into a gameplay mechanic.
Phoenix Wright
He was originally planned to be put into Tatsunoko but was caught because of some bullshit language thing. Let's fix this! He's video games' only playable lawyer, or at least the only cool one.
Bionic Commando
For some reason Capcom is dead set on reviving this franchise, which I don't really get. Regardless the grappling hook and gun combo is pretty hardcore. Also I dig the Duke Nukem look of the character, so maybe I just lack the nostalgic connection with the guy to get super excited.
Wang-Tang
As a fan of Super Smash Bros. Power Stone to me has always been one of Capcom's best franchises. The characters were crazy, the levels were interactive, and in the second one you could build your own items. Of the whole cast Wang-Tang is the best for this game, he's fast, shoots lasers, and can turn into a super saiyen look-a-like. Capcom seems to like distancing itself from this franchise, and it's a crime that needs to be fixed.
Gouken
Gouken was a character that I felt Street Fighter 4 could not contain. There was so much to the story of this character that 4's game mechanics just held him back. Gouken deserves to be doing so many crazy moves, and only a vs. game gives him this kind of freedom. In 4 he's stuck just being slow and really technical. In MvC 3 he could live up to his story.
Sagat
Sagat is too cheap in Street Fighter 4. Keep him exactly the way he is and put him in MvC 3 then maybe he'll be fair.
Leon Kennedy
For the life of me I can't figure out why Chris is in this game. Leon is way cooler and actually has moves. He has a ton of spin kicks and wrestling moves, and all Chris has is big punches. Granted those punches broke a boulder, but honestly Leon is just a way cooler character. Plus the fact that is so nimble makes him fit in better with the vs. Univese.
Haggar
The greatest mayor.
Scrooge McDuck
The very best Capcom NES game is Duck Tails. That's right I said it! Now you may be asking how Scrooge McDuck could be in this game, well I have the answer! Capcom made Duck Tails. Disney owns Duck Tails. Disney also owns Marvel. Now if all these forces work together then we'll have quite the cross over.
Ken from Street Fighter 2010
If any version of Ken is in this game it deserves to be this often forgotten spin-off character. Street Fighter 2010 honestly had nothing to do with anything else in the franchise, it just had the name slapped on to sell copies. Regardless it would be a nice bit of fan service, if at the least it was an alternate costume for Ken.
Vanessa Z. - P.N. 03
I never played P.N. 03, but I always wanted to. The game had a great Aesthetic, and a cool mechanic of combining rhythm and third person shooting. The main character was also cool looking which is reason enough to throw her into this game.
The Killer 7
This game never sold well, and is definitely a cult classic game. That alone is reason enough to throw them in some way. I imagine them playing like a violent version of Captain Commando or that evil character from Yatterman with all the henchmen.
In terms of final bosses the series has tried to always include something related to one of the companies involved. However they have never done a tag team fight with two bosses which I think would be awesome.
Wesker and Galactus are both characters who have never appeared in the series, and both are crazy awesome. Plus an ultimate team-up like that is what makes the vs. series so cool. It's two characters who could not even exist in the same universe teaming up for who knows why, and that's awesome.
I'm sure Capcom won't do this exact team, but I'm really hoping for a tag-team boss of a Marvel and Capcom character rather than just the multi-form bosses we've been given so many times.
The charcter count in the game right now is 30, but that's only who they have working. More are being added every day. However, to say that everyone from 2 will be in is extreme so here's my list of who needs to be kept in the sequel, excluding obvious ones like Chun-Li or Spider-Man.
Need to Keep: Excludes obvious ones like Spider-Man
Guile
Akuma
Cammy
Strider
SonSon
Captain Commando
Sakura
Zangief
Psylock
Cyclops
Venom
Juggernaut
*Replace Omega Red with Dr. Octopus*
Colossus