IGN sat down with Marvel's Chris Baker to see if he could explain more on the decision making behind Marvel'se side of alternates. You can read the article yourselves for detailed word for word of what he says. I'll just post the pics here starting with Phoenix as he did.
Phoenix:
(could have added the X)
Storm:
(X-Treme X-Men arena fight)
Dormammu:
M.O.D.O.K.:
Captain America:
He goes on to explain that Bucky Cap would look the same as Steve Cap while standing so they decided to leave him out. Also that his V shape would have been hard for designers to make without messing up the character (lame excuse). Also Said the complete change in Punisher Cap was all Capcom's doing. He said they decided on their own to take away wings, change head A to a star and Chest to a skull.... At the end of the day, Capcom decided who they wanted to have real different suits (Cap, Spidey, and a couple others).
I'm still praying Capcom makes DLC costumes like they do for SF4/SSF4. I'm still jealous Spidey and Cap has real different suits and Wolverine doesn't, lol. (and X-23 should have had her X-Force suit).