I made a post the Quests forum, I think it was, about a proposed mechanism for adding more aetherytes that would double as a gil sink + server wide project, and add missing aetherytes to some of the more obvious locations in the overworld in older zones.
(digs) Found it: 
https://forum.square-enix.com/ffxiv/...t-syle-project
Garlemald's upper map was the location that inspired the thread.
Urqopacha for sure could benefit - but like you said, maybe we will get one with the quests there.
The Ruby Sea could use one, although making that one work lore-wise would be rough.  It'd have to be built by the locals.  Maybe hidden in a sky island behind the volcano.
The far eastern side of Sea of Clouds is another. 
For those older zones, to prevent them from seeming too out of place, you could possibly lock access until flying is unlocked and MSQ is done for the base expansion, by having the aetheryte on a sky island or the top of an inaccessible from the ground building.  And the aetheryte itself remains invisible until a point in the MSQ where it makes sense to show it, although it wouldn't become attunable until a possible later point (they added the tech for this in Stormblood.)
That'd even work for the newer DT zones - you can't unlock Yak'tel's hidden aetheryte until after you finish base 7.0 MSQ (and the local Mamool Ja are grumbling about the outsiders, but accept the help because who doesn't want more aetherytes?)