Because it's a half assed attempt at pleasing the fans, and its only agitating them more.
ANY verison of MEGA MAN should have been included from the start, before even Zero.
Its simply that with all the [parasitic bomb] going down with Mega Man, its poor timing. People are already upset at the cancellation of 2 Mega Man games due to unspecified "criteria", and the prospect of the one Mega Man game still in development staying Korea exclusive. So they look to MVC3 to add a Mega Man to the game, a character that was in the top few requested, and instead, they give us a costume of the character.
It just stings. Its like they are avoiding using a Mega Man playable character on purpose. And again, dont really give adequate reasons as to why.
You asked about obligation. They dont have an "obligation" to add him. But you would think that they would listen to fan demand. We got Phoenix Wright that way didnt we? by fan demand? So why not Megaman/X due to fan demand? obviously they are open to it. And you would think that adding X would be a good idea to soothe over the fanbase which is still heated over what they consider to be "Capcom killing Megaman" or whatever else thats being said. Especially when Capcom has added other popular characters, except Megaman or X.
TL;DR
People wanted playable X, not a costume swap, and the way Capcom seems to be shafting Mega Man, the actual main character of the franchise, just hurts. Especially since X has never been in a fighting game, and has been so damn requested.