According to some sources, Doctor Doom and Iron Man were meant to be in the game, but due to rights issues could not make the roster. Cyclops and Omega Red replaced them instead.
This game, along with Capcom's other X-Men fighting games, were planned to be included in Marvel vs. Capcom Origins. However, rights issues, and the fact Capcom didn't see Marvel Super Heroes vs. Street Fighter as "good enough", prevented them from doing so.
Blackheart was apparently going to have a super where he summoned his father Mephisto, who appears as a draconic giant that grabs the opponent and breathes fire on them. Mephisto would make it as a red Blackheart Palette Swap in the main game.