"[I] was told that the boss battles that have been a Mega Man staple for years will indeed return, though the Capcom representative I spoke with was hesitant to explain how it will work. From what I can gather, the robot masters will come around for the ride but there will be some surprises along the way."
"..my concerns with Mega Man Universe at this point in time are the game's controls. If you remember the old days with Mega Man, you'll know that tapping the d-pad will make the Blue Bomber perform his epic shuffle to the side, which is great for sticky situations and tough jumps. But in Mega Man Universe, tapping the d-pad does nothing. It seems like Mega Man's movements are stiffer than they should be, but considering how early the game is right now, I'd say this issue is going to be addressed.
I wouldn't worry too much about the controls -- this is, after all, a beta build of a game slated for a 2011 release. Capcom's got plenty of time to make the necessary adjustments.
Any speculations as to what the Robot Master surprises will be? I've got a hunch that defeating a them would not only warrant their weapon but a set of parts, too, for us in character construction. Just my two cents, who knows. Anyway, you can read the full preview at IGN.