I pre-orderd and took home both the XBOX 360 and Wii versions of Marvel Ultimate Alliance 2.
We'll get one thing right off the bat. In terms of comparing to the original MUA game, graphics and gameplay-wise, the Wii version would be more akin to MUA v1.5 (whereas the 360 and PS3 version make use of the improved engine).
Both versions have done away with the skill trees, and now each character has only 4 activated abilities, and a host of more passive abilities. On the 360, these are channeled by holding in the Right-Trigger and pressing A, B, X, or Y. On the Wii, these are performed by simply pressing Up, Down, Left, or Right on the D-Pad (Wii Remote).
Both versions go through pretty much the same story line, but the Wii version has a few different/modified levels. The essence of the plot is the same.
For some of the Fusions and boss battles, we found it tricky sometimes to point the Targeted Fusions and make heads or tails of "where am I" during multiplayer on the 360 version since the angle is brought a little lower to try to show off the very crisp and fine HD graphics we all know and love. The Wii version for the most part retains the top-down view of the original MUA (as it seems to be running on the same engine), and Targeted Fusions are performed effortlessly by aiming at the screen with the Wii Remote (game play will "bullet-time" slo-mo while you aim the on-screen cursor, the aiming on the 360 is done in realtime).
The XBOX 360 version (along with PS3) has online multiplayer support, but the Wii version is local-only. There is a feature to send messages to Wii Friends with your scores on levels for them to try to beat, but I don't find it too useful. (I'd much have them over playing multiplayer anyways).
Some of the changes the Wii version has from it's previous installment: in addition to now using powers with the D-Pad, changing characters is now done with the "+" and "-" buttons. Pausing is now done with the "2" button. For a much beloved change over the original, you must now hold down "1" while manipulating the remote to change camera, instead of it moving automatically (which from personal experience used to be a big problem with four people playing).
For Solo play and online multiplayer, the XBOX 360 (and PS3) versions can't be beat. You will enjoy the epic storyline with MUCH improved graphics over the original game, and online play works great when friends don't feel like leaving the house. That being said, despite lacking any sort of online play, the Wii version just "feels" more like a Multiplayer experience than the HD counterparts. During multiplayer on the 360 version I had to put up with not-so-patient teammates edging us to move forward and blow stuff up while I tried to take in the beauty of the game. I didn't have much luck with that. The Wii version has a less intrusive camera during boss fights (it's not trying to show off the graphics or anything), and the aiming mechanism works perfectly with the Wii Remote. I did not play the original MUA on the 360 so I can not compare the controls, but they did not seem as "intuitive" as I was expecting (though that can probably just be blamed on how the L and R buttons are set up on the 360 controller, I much prefer their setup on the Playstation 3 controllers). In short I find ourselves playing through the Wii version when friends come over, and playing the 360 version solo once everyone takes off (now I get to enjoy the scenery!).
My final analysis:
Friends that don't like to visit, solo play = HD versions.
Gamer buddies getting together to blow stuff up = Wii.