!WARNING PERSONA 4 ARENA STORY SPECULATION AND THEORIES! SPOILERS ARE BOUND
This is me just guessing but chances are P3 MC will come back through Nyarlathotep, probably give him his old memories back and a new name, like they did with Tatsuya. Philemon is probably the master mind behind all this again, not surprising though. Going by P4A story, P5 will either be a new set of students with a mix of returning P3/P4/ characters, Maybe going back to big casts in persona games? So the game leaves us with hints of P3 MC, also known as Arisato Minato comming back soon.