Atlus has pretty much come out to say many times that they are in full support of Nintendo. Persona 4 Golden (my favorite game ever, btw) might have been on the Vita, but Persona is highly marketable and it's likely it could receive ports to a Nintendo console.
If not, at least we get what we have and SMT4, the true sequel to the main series (the one everyone wanted) is a Nintendo exclusive. That honestly says a lot. That's even bigger than bayonetta 2 being an exclusive in my eyes.