Well, as a Nintendo fan obviously I'd rather they be under my preferred company's umbrella haha.
Retro can't seem to make a damn thing these days and they're already tasked with Metroid Prime 4.
It would also make sense to fall under Nintendo however i just don't think Nintendo have anything for them to work on outside DKC. Microsoft house all their IPs and it would be only fitting to see the OG Devs retire making one more Banjo or Conker game. I am wishful thinking here. Either way, it would be a good outcome for Playtonic.
The first Yooka Laylee I thought was decent but uneven, so I'm not super sold on them doing a new Banjo or Conker, but Yooka Laylee and the Impossible Lair was superb, and very similar to DKC, which is why I'd feel more confident in them handling that.