Check out this interview with Marvel Ultimate Alliance 2 lead writer Evan Skolnick (no relation to Revenge of the Nerds' Louis Skolnick) as he talks about the game's story aspects. Heavily based on Marvel's "Civil War" crossover event, MUA2 deals with a schism among the heroes in the Marvel Universe. Players have to ask themselves, "What side are you on? Is security more important than liberty?" The answer will determine the game's experience, and whether the selected heroes are government agents or outlaws.
Along with the game's core concept, Skolnick discusses the challenges of writing a story for a game with 24 playable characters and working with voice actors to quickly alter the script.
Personally, I don't think there are any heroes or villains. Everyone is a skrull...whether they know it or not.