Lahabrea implies that the disaster which warped the Amaurotine's magic and created the Terminus is coming back. The Amaurotine's heard a "sound" coming from within the planet, and that the planet itself was "sick". Then, they wove a new life into the core of the planet: Zodiark and Hydaelyn. Now Hydaelyn is the only remaining "being" inside the planet. Guess who is losing strength as the MSQ progresses, to the point where she hardly even interacts with her chosen champion anymore?
I think that when Hydaelyn was "created", the Amaurotines personified the will of the planet, which was already sick or vulnerable to whatever the "sickness" is. "Hydaelyn" is just what Lahabrea refers to as the core of the planet. The sickness or the cause of the sickness predates Hydaelyn's "creation" and hasn't been fixed.
Lahabrea talks about "removing" Hydaelyn, (ie, removing the heart/core of the planet), but can life on the planet survive without the core of the planet? Unless he intends to simply replace the planet's persona of Hydaelyn with that of Zodiark, but that doesn't change the fact that the planet is still sick.
perhaps it is the overuse of aether? I'm guessing that the next expansion will tie heavily into the conservation themes of FFVII. Also, I fully expect the laws of physics to start breaking down and for some wacky high concept zones to show up.