The Ice Climbers never had a new game since the 1980's but still appeared due to being Sakurai's favorite game. With Infuane gone, the future for Mega Man is uncertain. However, Jim Sterling from Game Radar said it's a good thing.
I've heard Capcom will help out with the development of the Smash Bros. titles for the Wii U and 3DS, which means a slight possibility of Mega Man to appear to make up his absence in MVC3, or it could be Ryu. Of course it won't matter because I expect certain music to be used out of their appearance (Mega Man: Elec Man's Stage , Ryu: Guile's Theme).
Kinda disappointing that Mega Man got axed for MVC3. They got Zero and Tron to represent the most popular branch offs of the series yet no sign of the blue bomber himself. The fact that Legends 3 and Universe got cancelled made matters worse.