Atus has shown equal love with both companies, especially with exclusive games that are so good. I'll make it short and sweet.
Sony - Home of the Persona series and great multiplatform shared with Microsoft.
Nintendo - Epic Atlus handheld games always coming with bonus goodies.....Not really big on Nintendo's consoles besides Shin Megami Tense X Fire Emblem.
I actually chose Sony because they never failed on a Sony platform, the Persona series is just so godlike it doesn't go multiplatform................God damn i have a feeling Persona 5 will be Multiplatform with Xbox One just like FF15 & KH3.
But if Nintendo wants to stand a chance against their competitors especially the doom & gloom they are getting week by week, it would be smart of them to buy Atlus as quickly as possible, because I know Sony has their eye on them and will eventually strike a move with Atlus in this year's Tokyo Game Show.