Mega Man games seem to go over better when they stick to their 8-bit roots, but there's no reason why they can't be 8-bit-ish while operating on all three axes. Just take a look at Mega Man 8-bit Deathmatch, a game that takes the sprites from the original Mega Man games and pastes them onto a Doom-like engine. It may be a little hard on the eyes for those who prefer the "realistic" look utilized in most FPSs, but I bet Mega Man fans of old would rather play this than Call of Duty.
If Valve could put the official stamp on the fan-created Half-Life mod Counter-Strike and permit it to become a "real" game, I don't see why Capcom couldn't let this title go to WiiWare/PSN/XBLA as a $5 download. I know I'd buy it.