Capcom has some strong IPs that would be great as Nintendo exclusives for sure, such as Mega Man, Street Fighter, Resident Evil, Monster Hunter etc.
Not to mention some long abandoned ones that I'm sure many would like to see come back, like Ghouls n Ghosts, Gargoyle's Quest, Final Fight, Darkstalkers, Power Stone, Breath of Fire (a REAL comeback, not shitty cell phone games), Maximo, Onimusha, Viewtiful Joe, etc. etc. etc. etc.
But I'm not sure how willing Nintendo would be to buy up a big company like that. They certainly passed on Atlus. The studios they've "bought" in the past, or made exclusive deals with, have tended to be smaller, such as Monolith, Retro, Next Level Games, etc.
It would be cool to see, in a way, especially because Capcom has really sucked for the most part over the last 10+ years. But I don't know that we'd see it happen.