We discussed your thoughts on it when I was over at your house, YJG.  I understand a lot of them, but your gripes about B&B combos are kind of lost on me.  I really don't feel that these characters control alike--while your basic air combo is nearly universal, actual mind games and proper use of each character goes far beyond the basic S > L > L > M > M > H > 3H > HC combo that you can pull off with so many of the characters.  The ridiculous variety and unusual choices make for a game that has 35 characters who handle differently and control different areas of the screen, as opposed to a 56-strong cast where a good fourth of them are either palette swaps or serve no real purpose in competitive play.
Which brings me to my real point on this: competitive play.  If you watch competitive MvC2 play, you'll see the same four or five characters being brought out, because they're that much more powerful than everybody else and it's insane.  However, you then watch MvC3 play, and you've got Justin Wong using Thor and his command throw, you've got Combofiend beasting with Spencer, you've got Clockwork using plain ol' Phoenix and not going for a Phoenix Gambit like so many other players you'll find online.  I can't wait to see what happens if Umehara Daigo ever enters the competitive scene for this title.
Yes, that was a lot of fighting game jargon.  But I think it goes to show that THAT's who this game was made for: the people who will take the time to work at it and actually see beyond "who's in it."  Mega Man X wouldn't add anything to the game that we haven't already seen before with the original Blue Bomber, but Zero brings us a fast-paced rushdown character with a Genei-alike.  I'd much rather have a weird choice (M.O.D.O.K.!) who plays so much differently from everything else I've ever used in a Capcom fighting game than another one-trick pony like Gambit in the few games he was in.
Finally, a lot of the Marvel choices went for characters who have been getting a lot of face time in current comics.  Just like MvC2 had Marrow and the Psimitar-wielding Cable due to the X-books being at the forefront in the late '90s, MvC3 has plenty of Avengers characters thanks to universe-spanning crossovers like Civil War and Siege.  My only real question: where's the Sentry?
-Anonymooo