I feel the problem with aether currents is that people who love exploration will explore with or without locking flying behind the currents; people who don't enjoy exploration simply feel like they're being forced to waste time.
Being a theme park MMO where players are expected to pick and choose the parts of the content they like, I would agree that aether currents isn't something important enough to force on to all players (e.g. MSQ is something important enough, PVP isn't, crafting isn't, housing isn't, and nor is exploration).
I would say a good compromise is to keep aether currents and use them for something else, and unlock flying at the end of the MSQ for the zone. Aether currents can be used to unlock maybe extra toys (like consumable toys one can buy using the FATE currency?) or even extra aether shards that only work for in-zone teleporting.