Off the top of my head for 360/PS3 (everything I've seen about the Wii version is garbage since VV/Activision handed it off to another developer)
- Fusions are the huge one; going to be a lot of fun co-ordinating these with friends
- Better online play (multiple people on one console can play with others over online)
- AI takes over your character while choosing skills in multiplayer play so you don't hold up the game for everyone like in the first
- Ability to swap characters in and out at any time without having to go to save points
- Chat options with NPC's affect Team Boosts you gain
- Equipment seems to be gone and replaced with the boost system as well
- Abilities when putting in points also upgrade them; this was done to an extent in the first one but it seems to be more so in this game. ex. upgrading gambits staff swing will pop enemies up in the air
- More enemies on screen at a time
- Replayability; You choose a side during the civil war and you gain abilities as you level up that maybe only specific to that side, same with costumes
- Only one alt costume per character, but costumes are more than just a reskin in this one as they are actually completely new models with more detail
- DLC is not an afterthought like with the first one, they have said they are already working on DLC packs so lets hope for lots of them. IMO I think one of the first DLC packs we'll see is the Wii/PS2 and DS exclusives for 360/PS3.
- More difficulty modes
Fan Service (info on that here:
http://www.comicbookresources.com/?page=article&id=22574 ):
- Audio logs which provide backstory to the secret war and civil war: "Numerous audio logs provide critical pieces of the backstory, while hundreds of dossiers provide information on every conceivable topic, ranging from organizations to locations to characters."
- Trivia is returning and is now multiplayer

- Unlockable concept art is returning
Here's some recent gameplay videos:
http://www.youtube.com/watch?v=elR1HrebTuw&feature=channel_page
and 12 minutes with the game
http://www.gamespot.com/xbox360/rpg...sents-now-playing--marvel-ultimate-alliance-2
edit: oh and here's a video of the Wii version which will show you how disappointing it is, it looks worse than MUA1 on Wii and it pretty much reuses all the assets of the first one. N-Space really dropped the ball on the Wii version :
http://www.youtube.com/watch?v=BaBAm72SsJc