There's the possibility female representation on Marvel's side from the Thor series. Sif, Hela or maybe even that female Thor featured recently.
Howard the Duck and Machine Man seem like good candidates. Neither have been in the MvC fighting series before, I don't think. Odin would be kind of cool, same with Loki. War Machine is probably going to come back as a standalone character + the Iron Patriot as his alt costume swap.
Eh, could see Capcom go completely nuts with DLC costumes if they wanted to. Just the number of variations that have graced comic covers over the years, the movies, and just Iron Man's different armors alone ... it's hard not to think about.
My completely crackpot roster choice (which would itself require extra licensing) would be Ash Williams on the Marvel side (since he was in the Marvel Zombies vs. Army of Darkness crossover).