Who knows, they could still make games for Capcom, but now they're not limited to Capcom's rules and boundaries. I'm sure they didn't want to make 5 Viewtiful Joe games over 3 years. Of course, going independant is likely to put a damper on their financial backing, but I think their reputation should be good enough for a major company to sign them on for a game.

I see Microsoft in their near future.