With Baker's help, Capcom added some alternate costumes ranging from the familiar (Spider-Man's black symbiote costume, Iron Man's all-silver '60s "Tin Can" look) to the obscure (the "Iron Spider-Man" look, above, from the Civil War series, or Wolverine's suit from Age of Apocalypse). The costumes aren't perfect, since the shape of the 3D models can't be altered -- they can only be reskinned.
We said Marvel "mostly" avoided the random Marvel vs. Capcom 2 variants. There's one really important exception: a blue Magneto costume was added specifically as a reference to the famous "Mahvel Baybee" video. Old school!