Well, the existence of Ultimate MvC3 has been justified in that the Japan earthquake several months ago threw off their development schedule. They originally intended the additional characters to be DLC for the original game, but since that didn't happen, they instead decided to bundle them all together and refine the mechanics and balance and release it all together as a new edition. It's not that great of a justification, and it sucks for early adopters of the original, but that's the excuse Capcom is sticking with.
Still doesn't explain the lack of Mega Man, though.