Like xelad1 said. Since they put all the effort to create 3D models of all the characters, IDK, maybe they would like to use them? Them Capcom fighters and Megaman are primarily 2D character models, which is why it would make sense to animate it that way. Also, we've already seen the Subspace Emisssary movies done in "traditional" 3D.
About anime....
Anime is a medium of expression. It is a way to tell a story, as broad as writing a novel or filming a Hollywood movie. The percieved "quality" of any specific anime series depends on the effort, care, and talent of its staff, the size of the production budget, and most of all, your personal preferences. Just as American telivision programs differ greatly in genre types, musical direction, style, and target audience, so do anime. It just happens that most anime that gets exposure on American cable networks are aimed for kids under 15-ish.
It is ignorant to make sweeping generalizations about anime other than "it is animated" and "it comes from Japan".