I think the Garleans are tools for Ascians, surpress their ability to use aether and keep telling them they're the superior race with unrivaled tech (which I believe that derided from late Allagan ingenuity) that needs to rule the "savages" that can use magic. The Garleans might have been used to control and conquer the masses all the while the Ascians would get the beastmen to summon primals (and a few willing participants) and keep the forces fighting amongst themselves.

Crackpot assumption: Those Garlean eyes are like Chekov's Gun... it has significance, but we don't know what it is. Aether suppression? Mini Sabik Hearts making them ticking time bombs? Ascians created the empire to further their own goals, and at some point they will outlive their usefulness and that's when we'll know the real secret about those jewels.