Their slate for the foreseeable future is pretty full: Persona 5, SMTIV, Etrian Odysset V, Odin Sphere, and 13 Sentinels. While still exciting, it's hard to believe they have even more up their sleeve.
Like many others here, I think it could be SMTV. Considering SMTIV: Final is an enhanced edition, I don't think it would be beyond the realm of possibility that the team has also had the next entry in the works.
It could also be a new entry in another sub-series like Devil Summer or Digital Devil, but I find this highly unlikely.
My hope is that it's a new IP. The last time Atlus internally developed a new IP we got the remarkable Catherine. I would love to see what else they're capable of!
And who is to say that these games are internal? Could easily be a collaboration with some like Arc System Works.