The only ones who I reasonably think could still be alive are The Great Gozu and Chisa. I really, REALLY hope it turns out that The Great Gozu is the mastermind, because:
1. It'd shock all of his fans
2. It'd be a huge table turn for those expecting a corpse to not be a corpse, but be wrong about which corpse it is
That said, you will not catch me complaining about Seiko secretly being alive.
I hope its not a "I faked my death" thing again, since that echo's Junko way to much (Then again, everything post DR1 is basically "Junko planned it all along",or people obsessed with her)
But if it is, it will probably be Chisa.