If Nintendo bought out the whole of Capcom (though I see individual IP purchases as the more likely matter), I feel there wouldn't be a huge amount of Capcom characters made playable within Super Smash Bros, at least outside of either the key ones or all at once. For such a matter we'd likely see a Capcom vs. Nintendo games wherein Nintendo could properly represent the vast amount of Capcom IPs they'd have obtained without side-lining the Nintendo additions for SSB.
They'd still have quite a few Capcom additions for SSB, having Mega Man stay and at least three more additions, but it wouldn't be done to completely overshadow the Nintendo additions... as in those not made by a recent purchase of Capcom (who of course would be at Nintendo in this scenario, but you get the idea).
I feel that they'd be quite limited by having to adhere to Sakurai's rulings, provided they haven't changed, such as 'No use of realistic guns', 'having had a game on a Nintendo system' as well as Sakurai's current 'no fighting game character' rule. This would work to bar quite a few of the Capcom IPs from playable spots if followed, instead relegating their inclusion to Assist Trophies, or even their own separate assist item, and other such things.
Without researching their IPs within detail, I'd believe the most likely ones to have playable spots of the Capcom IPs in this scenario would be the Mega Man series (of course), Ace Attorney, Ghosts n Goblins, and Monster Hunter (Capcom encountered problems with adding Monster Hunter to Marvel vs. Capcom but Sakurai has already shown he does not mind adding avatar characters into SSB). I can't remember all of the Capcom IPs off the top of my head (they have so many) but many that do come to mind encounter the obstacle of Sakurai's current rulings for character inclusions. If you know any other Capcom series with strong connections to Nintendo that obey Sakurai's current rulings, please do mention them to me if you have time.