SE try to always to counter the obvious theory, so a Zenos/Hydaelyn/Zodiark or a fusion between two or three seems to obvious.

I think we will get an unknown boss who will pop-up at the end like in many FF games.

It could be the Apocalypse creature itself, or why not a fusion of the Twelves summons like a test to see if the planet and his people deserve to continue to live or not (so it will be erase from the existence and time forever).