I'd assume Aetherite Crystals would be pretty useful in maintaining the levels of Aether in the local vicinity.

Given that the Garleans kind of don't want places turning into the Burn on accident, it would make sense that they wouldn't be in a rush to remove them from the empires they took over (Including, their own homeland after they lost it)

Also, don't count out the Garleans finding SOME use for them. Given they're always trying to either manipulate aether forcefully or study aether related tech to try and create some Magitek approximation.

So yeah, don't be surprised if you end up teleporting to an Aetherite Crystal that has a huge stonking Magitek machine hooked up to it for Garlean teleportation...