I used just about everyone from the playable roster of the first game on the 360, including all the unlockables and the DLC packs.
I tended to use Nick Fury, Moon Knight, Dr. Doom (thematic reasons) and Venom the least.
My favs were: Captain America, Iron Man, Spider-Man, Wolverine, Cyclops, Iceman, Sabretooth, Luke Cage, Storm, Black Panther, the whole Fantastic Four, Hawkeye, and Dr. Strange. I tried to rotate classic line-ups wherever possible (FF, X-MEN, Avengers, New Avengers, Defenders--- we needed Namor, etc.)
Coming up for the sequel, I really want to have more opportunities to assemble and mix-match classic rosters and line-ups, so I want everyone from the first game plus Namor, Black Knight, Hercules, Black Widow, Angel, Kitty Pryde, Jean Grey, Beast, Wonder Man, Hank Pym, etc.