A look at one authors opinion on what his ideal outcome for ATLUS would be given the circumstances.
Personally if we're talking 3rd party, I'd give it to GungHo. These guys struck it filthy rich not too long ago. It would be a perfect fit (If you don't know about them, look em up). For 1st party, I would like Sony. Sony's (company named "Aniplex") already distributing and producing Persona 3 The Movie with Atlus, and made Persona 4 the TV series for them. Plus the Persona 3 movie is going to be in multiple installments, so Sony already has work to continue with them in the long run. I know Nintendo has Fire Emblem x SMT, but I don't see games like Catherine being produced (financially and morally) by Nintendo/Iwata. Bayonetta...blah, blah, blah. Still it's more of a 2nd party type of endeavor since it is Platinum's IP. Either way, I still think i'd like to see Sony. Since Sony has their foot in the door for a couple of Atlus projects, Persona 4 is Yoshida's (of Sony) favorite game & Chie his favorite character (so i'm sure he's interested in Atlus), and I feel like there will be more freedom for Atlus to make what they want, and Sony wouldn't be fazed by products with such explicit content like Catherine or Shin Megami Tensei 2 (which had God (Yhwh) as the last boss). Yeah Nintendo didn't ban them when they were 3rd party, but Nintendo DID ban "The Binding of Isaac" so I'm not very confident about the integrity of Atlus's mature nature being kept fully intact under Nintendo. Better to have a third party, or Sony imo.
N4G is a community of gamers posting and discussing the latest game news. It’s part of NewsBoiler, a network of social news sites covering today’s pop culture.