Well, what we were able to hash out last night was that the aether a primal uses on the material plane is lost to some degree or other. The aether that constituted its physical form returns to the land, but other than that it's up in the air as to how much is preserved despite spinning the elemental wheel.

The first SMN quest implies that repeated summons or keeping a primal on the material plane for too long will warp the aetherial flow of the region to one favorable to a primal's element; that is to say, the Sagolii Desert is said to be a consequence of the amalj'aa summoning Ifrit more frequently than most other primals. However, this can be seen to some extent in most beastman strongholds. Given a primal's physical form is created using crystals of a given element (or elements), if a primal is killed the aether that made up their form will return to the nearby land... which would logically warp the surrounding land to that element.

I would postulate that elementals (sprites, not the Elementals who rule the Twelveswood) are a sort of attempt to bring things back to equilibrium - if enough sprites were created and migrated to areas deficient in their element, it would restore the natural balance. Just an idea, though. Other than that how the aetherial flow can naturally change is unknown.

It is possible to make aether incompatible with Hydaelyn, though - that's what corrupted aether is believed to be, and why it lingers around as corrupted crystals instead of doing something.

(Thanks to everyone who indulged me.)