I read this little tibet regarding Mega Man's exclusion in MvC3. This is an interview with Ryota Niitsuma, the game's producer:
"I assume you’re talking about the original Mega Man. There was a Mega Man slot for this game – we had room for a character from that series. But when it came to the propriety of that character being in a fighting game, Mega Man has some problems.
If we were to adapt the original Mega Man character into a fighting game he would have to have a lot more extra moves and abilities, and that would then create a different Mega Man entirely. You couldn’t retain his original character as he is. So we looked into other Mega Mans, and decided that Zero had the best list of moves already in existence when it comes to fitting into a fighting game."
I for one think this is utter bullshit. I mean, he says Mega Man isn't the hand-to-hand fighting type. Then why is Arthur in the game? All he does is throw lances and get stripped of his armor. How do you justify that?