Many people are commenting based on what they, personally, want. I'm going to look at it from a different perspective - which companies would benefit most from it.
In terms of first-party, Nintendo has the most to gain, as Atlus has quite a few dark franchises, which is what Nintendo is most lacking. Atlus would be able to function as a distinct branding for games that are... not so family-friendly, thereby protecting Nintendo's image and still catering to those who seek such games. It would also expand Nintendo's internal development capability, at a time when Nintendo has been having difficulty getting games out in a timely manner.
Microsoft also has some to gain, as they have a big Japan problem. The potential to rebrand in Japan, perhaps as the "Atlus One" or something like that, might help to improve sales there, especially if that goes along with a lineup of Atlus IPs that sends a clear message to the Japanese gamer. However, MS is unlikely to get it.
Sony would also gain, but their gain would be relatively small. The only notable positive would be that they would get some extra exclusivity, plus a few IPs that mostly appear on other platforms.
Of the three, I would expect Nintendo to be the most likely candidate. Their financial situation is strong (unlike Sony), their motivation is obvious, and their relationship with Atlus has recently been strengthened already.
Of the Japanese third parties, I think that Sega has the most to gain - their IPs would have good resonance, but not too much overlap. However, Sega also isn't exactly flush with cash; for those saying that Sammy can afford it, I point here, where it says that Sega Sammy has 18 billion yen in capital - they can't pay 20 billion yen for Atlus. I'd imagine that their bid was closer to 10 billion yen.
Square Enix, Capcom, Tecmo Koei, and Konami (EDIT: Oh, and Marvelous) aren't likely candidates, in my view, due to overlap in the IPs. Atlus just doesn't represent enough value to any of these companies.
Namco Bandai is a possibility, I think, and it's hard to find solid numbers, but it appears that they have the cash to do it. There is some overlap, as I see it, but not too much. I'd probably call this the frontrunner in terms of gaming companies.
For western publishers, I'd start by suggesting that Ubisoft aren't likely at all - not that they couldn't do it, or that it wouldn't have value, but that I think it lacks resonance. Activision and EA are more likely - both have the cash, I think, and they wouldn't care about resonance. Disney and WB aren't going to do it, in my opinion. But perhaps the most interesting case is Take Two - they'd have the money, they'd probably be interested, they have better resonance than Activision or EA, and there's no real overlap.
So I'd suggest Namco Bandai as most likely, followed by Take Two and Nintendo. Of course, I could be WAY off. But that's how I read it.
