Given that the independence of Atlus is what allows them to put out such a large amount of games with such a large variety, I wouldn't be thrilled with any major company purchasing them. If I had to pick a large company to do so, I'd side with Sony just because they aren't huge micro-managers, whereas Nintendo is. I'd still prefer a smaller company like Gung-Ho or XSEED acquire them, though.
Sony has a nasty habit of shuttering studios in recent years (Psygnosis/Studio Liverpool, BigBig, Zipper, Ingocnito, etc) plus they invest next to nothing into the Japanese industry these days. SCE has actually never bought a Japanese studio, they simply don't appear to value their home development community and seemingly prefer chasing Microsoft westward.
Nintendo's "iron fist" developer policies are also largely overblown, and is traditionally a western phenomenon anyway. Within Japan Nintendo funds a multitude of studios on a wide variety of projects, many with little oversight. If you look at the last Japanese studio they acquired (Monolith Soft) they're flourising these days with a lot of backing and a lot of discretion on the projects they want to do. Nintendo would easily be preferable to Sony for acquiring Atlus imo, and their track record really supports it.
Sony doesn't have to buy Japanese development when most of that community (especially the JRPG guys who they have wrapped n their hand) supports them anyway.
Sony buying Atlus would just solidify what platforms other niche japanese developers would develop for. (not that they plan to leave the PS3 any time soon mind you)
Also to say Sony doesn't invest in Japnese studios is disingenuous Looking at thier output as of late.
-Gravity Rush
-Tokyo Jungle
-Soul Sacrifice
-Rain
-Puppeteer
-Destiney of Spirits
-Knack
-Freedsom Wars
-The Last Guardian
-Gran Turismo 6
-H
Most of those games are made in conjunction with non sony Japanese Studios.
Nintendo's Iron Fist isn't vastly overblown. If that were thr case than where is a New IP from the Zelda team or one of the Mario Teams. Why didn't retro have free range to do whatever they wanted for their next project. Why is Sakurai wasting his talents on yet another smash bros game that he didn't even know he was making.
(Its even more funny when one branch of Sony's