Capcom's Japanese site has a poll up for users to vote on what system MegaMan games should go on in the future.
http://www.capcom.co.jp/rockman20th/
The poll's on the right side of the page. The only two important options are in English, so it's no problem!
I voted PS3.
[spoiler]But not really.[/spoiler]
Wii seems like a given. If it was on the 360 it'd probably turn out like Bomberman Zero and if it was on the PS3 it wouldn't sell.
I voted for PS3. I know the 360 won't win in a Japanese poll (apparently, nobody has picked it yet), so voting for that one is futile. Since I would've picked either the 360 or PS3 (assuming Trophies from Home would be available by then), it makes the choice easier. Lastly, it's up in the air whether or not new Mega Man games will be 2D or 3D, and while one must suffer through 2D games with the 360 thumbstick and crappy d-pad, the PS3 Sixaxis offers good controls for either dimension.
Also, I figure Mega Man would show up in some shape or form on the Wii regardless since the system is selling across the world, so I'm pushing for a truly next-gen Mega Man experience (Legends 3, perhaps?), and it's only fitting to see it on the series home.