It makes no sense from a lore perspective. We’re following our own aether trails using our own magical ability. Not to mention, who are we even paying? Is Hydaelyn rifling through our pockets?
It makes no sense from a gameplay perspective. The paltry sums (topping out at 999g) are inconsequential, and far less than what we’d earn from a leve or quest, even as early as level 10. If the intent was to make teleportation a rare thing when you needed to go from one region to the next, the price should have been higher from the get-go. As it stands, it’s basically free, with players (myself included) teleporting with great frequency.
So why is there still a gil fee associated with teleportation via aetheryte? As far as I can tell, it’s just a holdover from 1.0 that no longer serves any purpose.