First Nintendo is paying Capcom for using Mega Man, just like they are with Sonic...Pac-Man most likely, but with Namco helping to make SSB 4 they might make an exception. As for Nintendo never buying an ip from a 3rd party, don't ask them about Fatal Frame.
It's good to be king...unless Mario's chasing you Pokemon Black 2752-0405-8925
Mega Man would be great as a Nintendo property. I would even go for a series reboot to fix plot inconsistencies (particularly the X Series, which is a cluster**** of plot holes).
It shouldn't be a drastic reboot though. Character designs, music and gameplay should be the same (don't mess with what works), just remake levels and fix the plot holes.
Although, I think if Nintendo got control of Mega Man, they should merge with Keiji Inafune's Comcept studio and Inafune can "have his baby back". Then he can merge Mighty No. 9 with Mega Man and BOTH would be owned by Nintendo.
Since I always immediately associate Mega Man with the NES and SNES I think he would be better off there. They could just keep making side-scrolling platformers. Mega Man 9 and 10 weren't so bad. I would even enjoy seeing a Mega Man "metroidvania" type game come out with the whole Super Metroid / SOTN exploration while obtaining various enemy abilities.