Well so far Nintendo has shown much more respect to Mega Man over the past few years than Capcom has, so I really wouldn't mind that. Did you see the Smash Bros tournament and the crowd reaction to his final smash? As a long-time fan, I have to say that I get a big stupid smile on my face every time I see it.
Not to mention that Monster Hunter is probably Capcom's biggest cash cow in their homeland, and since MH has been doing pretty well on Nintendo platforms I think it'd be hard for them to pass that up. Ideally I'd want a Japanese third party like Sega or Konami to scoop them up, but on the off chance that Capcom does have to sell off their property or be bought, I don't think Nintendo would do a bad job with them.