There are a number of points that hint in that direction
Overall though the game doesn't give that much room for speculation; the few topics that you might expect to come up in the future are discussed so glancingly that there's not much to say about them. I'm still bummed you don't get to look at any old records at Basel University or Aramis.
Finished the game and oh boy was that... something.
- I'm kind of surprised we didn't get any resolution on Nina obviously working with some other party, especially since one of the missable downtime segments involves you walking into her having a conversation; I was really expecting a last-minute twist there if nothing else. Also, that line of hers she practices in her last Connect event sounds almost like something she's preparing to say to Judith whenever her secret comes out...
- Falcom seems to be teasing us with (S-?)Crafts for Kasim, Ortesia and Rion in the barrier-breaking scene. That sequence reminded me a lot of the approach to Pandora in Tokyo Xanadu.
- With the Pandemonium effect stopping time for most people, time rewinding to revive the pillars around Genesis Tower and the countdown starting to reverse once we enter it, the clock motif the tower itself shows off, and several dead Almata members showing up again (without Gerard's excuse) we're definitely dealing with the Sept-Terrion of Time here, which means Falcom pulled another G. Nome on us with クロノキセキ.
- Vagrants=Zion, huh? I'm going to have to go back to the conversation sequence again because between the katakana shenanigans and being extremely late when I finished, I only caught about half of what he was saying and as the end of Zero would prove after the fact, that stuff can be Important.
- That ending sequence was incredible.