Much as I hate what Capcom has done to themselves, I wouldn't want them to be bought out/go out of business. Nintendo won't be buying the entirety of Capcom; that much I am sure about. It'll likely be someone who cares a lot less about gaming.
If Capcom goes out of business, the franchise will be going in all different direction. I'd imagine that Street Fighter would go to Namco for one. If Platinum Games has money, they might go after Okami/Viewitful Joe/Devil May Cry. Nintendo may get a couple of franchises; Phoenix Wright and Monster Hunter comes to mind. Maybe Konami could get Resident Evil if they can afford it (not sure about financial situation here)?
Unfortunately, I see Mega Man falling through the cracks. I don't think anyone will be there to save him; Nintendo would prioritize Monster Hunter and Phoenix Wright if they go for anything, Comcept probably can't afford to get Mega Man (and even then, Mighty No. 9 is Inafune's new baby, which mind you, is looking great) and I can't think of another other companies that could buy a franchise out would be interested in a franchise that has generally sold poorly in recent years.
At least he got in Smash when he had the chance, though; so he won't be forgotten.
Speaking of which, what exactly does happen to an IP if a company who holds it goes out of business and no one takes the IP? I've been curious about this and I am not sure how this works. That said, I think Capcom will stick around until at least the end of this generation so I still have hope that they'll pull themselves together.