I agree with the homepoint reasoning with leves. And I like the idea of 'restoring' aetherytes via quests (even if it doesn't do anything about the leve failure issue NOW, it'd at least improve that condition in the future).

As a temporary measure, how about adding the gates of Idyllshire as aetheryte net points? Similar to how gates are treated in the three main cities, I mean. While it wouldn't solve the "two loading screens" issue, it would mean you wouldn't have to run all the way to the gate.