For Marvel characters, Doctor Octopus is the only one we know of that almost actually made it into the game. According to Niitsuma, alot of him was complete, including his theme and was just about ready for the game. That being said, I don't know if he ever mentioned why he didn't get in. It's sad and it sucks cause MvC needs Spiderman villains.
Kingpin is another that was considered, but Modok was favored over him for being more potentially unique. And last, as someone mentioned, Blade was considered as well, but wasn't chosen because of being similar to Dante. I think a couple others were mentioned as well, but I can't remember them at the moment.