Never said it would, but the notion that everything is just fine and dandy with Capcom if they keep on their current track isn't necessarily accurate, and it wouldn't be surprising to me if they would at least entertain the notion of a buyout from one of the big three.
But, hypothetically speaking, both companies (Capcom and Nintendo) could feasibly gain quite a bit from such a partnership. Capcom would gain some financial security from Nintendo's coffers (and won't have to dedicate massive budgets it soon may not be able to afford on PS4 and XB1 game development), and Nintendo gets what could potentially be a system seller of a studio on its books. It's not difficult to imagine some partnership where Capcom essentially becomes Nintendo's "mature" developer focused purely on making games for the "core" audience, while Nintendo focuses on making its family-friendly Mario and Zelda titles. What's more, with Nintendo handling the publishing, they'll no doubt put they foot down on Capcom's more shady practices (like on-disc DLC) and clean up the studio's image in the eyes of the consumer. Not saying such a merger wouldn't be risky, but from that perspective, it's kind of win-win for both companies.
Like I said, that's hypothetically speaking. I'm not saying it's ever going to happen, just that - on paper, at least - it's something that could potentially work.