So that's where Viewtiful Joe 3 went. Capcom and developer Clover have announced that the two groups are heading their separate ways, with Capcom going off to create more Resident Evil and Mega Man spin-offs and Clover becoming its own company as opposed to just another division within Capcom. Wired has the news (some folks are claiming that Capcom has liquidated Clover, but it looks as though the group may live on).
A source who wishes to remain anonymous is telling me that the Clover gang actually wants to split from Capcom and form their own independent development studio. So the dissolution, then, would have been caused by the developers deciding to take off.
Good luck to you, Clover gang. I can't say I've ever been overly impressed by a Clover-designed game, but a lot of gamers hold the group in high esteem. Greatness has to start somewhere.