My personal opinion is the primals will probably still exist in the storyline, even if they're not quite the same world-ending threats that they used to be. The knowledge on how to summon them is still out there, and while the issues with Eorzea and their beast tribes are settled for the moment, the game's pretty clear on the idea that people fall back into despair, cruelty, and fanaticism eventually. It is worth noting that the presence of the scales means that any Scions or future party members could join us in fighting them now, meaning they can be relegated to dungeon bosses rather than full Trials. Even if we go to the New World or Meracydia we could have primals to slay.