If there showed any interest there could be a nintendo vs capcom, though unlikely at this point. Nintendo vs DOA would be more likely if only by a hair's breadth. I say this cuz you never know what the future brings. Certainly never thought I'd see a sonic vs mario game. Crossovers are always good. MvC 2 has stayed strong all these years. Can't say the same of its successor, though.
Why you think would they not bother with M.E.?