If we're seriously debating what company between Sony and Nintendo would buy them, I'd think the latter would acquire them, because:
Atlus is developing many titles on 3DS, and all of them saw good, if not great, sales in homecountry (and good sales over here too)
Actually, the only Atlus brand not on Nintendo platforms now seems to be Persona (+ Catherine)
There are good possibilities Nintendo is publishing SMTIV in Europe and, above all, they're developing SMT x FE
Nintendo is much more Japanese-centric than Sony right now (Sony didn't even obtain to have FFXV and KH3 as PS4 esclusives, after all. Not that this increases so much Xbox One's chances in Japan, but still), and they already demonstrated they're not so against such operations (Bayonetta 2 it's a niche title after all, and its Japanese sales are around those of many big Atlus releases).
But still, I firmly believe neither of them will buy Atlus. In the case, it wouldn't be Sony.