In the very beginning (or, well, close to the beginning), Lahabrea commented that Hydaelyn was indeed a "parasite" responsible for "aetheric disturbances [threatening] to warp aetheric and natural law beyond all recognition," and that She needed to be "burned out if the planet is to recover."
While it's easy to forget this and/or dismiss it as bunk... if Solus speaks truth, it's been there from the very beginning, up with Ifrit's comment that he couldn't temper us because "[our] soul had already been claimed by another." (Of course, given Hydaelyn hasn't used her claim on our soul to compel us to actually do anything, it feels more like an inoculation against other primal influences.)
So. F/GO Babylonia-style rebellion against Mom incoming? And we still don't know why the Ascians serve Zodiark and consider him the "one true god," if he too is a primal like Hydaelyn...