Personally I'm gunning for the following, for starters:
With X finally in a fighting game, who better to have him square off against than Vile? I suspect Sigma is either already given as a playable character, or is relegated to being part of the final boss package with Ultron. As for Fou-Lu, I wanted some representation from the Breath of Fire games for the first time, but I figured the main character would make it confusing since we already have Ryu from Street Fighter in there, so maybe not. I'd also be fine with Nina from Breath of Fire I, who uses a rapier in battle and looks the cutest and most battle-ready of the series.
-(Old) Nick Fury
Old Nick Fury's unlikely, but I think he'd be fun alongside Cable or Deadpool. Rocket w/ Groot and Star Lord seem the most likely, especially since rumors from NeoGAF suggest Groot will serve as an "assist-like" character. Star Lord would be an interesting character to play with, considering his lack of obvious superpowers other than the space-ready techno-mask and ray guns.