What do you mean alternate endings?
And was this prophecy mentioned in XIII-2?
I don't remember it...
Sorry, that was semi-sarcasm on my part.
What with the premise of Lightning Returns being you can't discover everything on the first playthrough, and since FFXIII-2 had alternate endings (Paradox Endings) it's a possibility that shouldn't be ruled out.
But if you want more specific stuff:
1. Snow is a L'Cie and that could be a BAD thing at this point (given what we know happened to characters in FF Type Zero/Agito).
2. Noel inherited the Heart of Etro (maybe?) from Caius.
3. Lightning is WHO you play, so it could have a bad ending possibility.
I could say more about the others, but that's...just a bunch of things to consider and mostly speculation.
And yes there was a prophecy in XIII-2 but it mentioned 2 saviors, not just 1.