I mean you can say that last line to the end of everything, doesn't make it true.
Forumaccount has provided no logical argument why it has to be removed.
This is fun. . .
I've seen quite a few arguments on the purpose of the system, you just don't think it does it adequately or don't personally value it. Both of those don't mean it wasn't a reason given. And with many systems there are often ways to circumvent them, this doesn't mean they've no purpose (like emergency valves.. super important). Many tax solutions don't adequately or fairly do what they're intended, doesn't mean we shouldn't have taxes. Just because some people don't like something doesn't mean it shouldn't exist. Although, it does raise the fair question "should it?" or "can we make it better?", but that's a question not an obligation to change- like I'm answering "yes it has a purpose, I might be interested in other variations that attempt to do what it does, but its purpose I find important and would not want flying to simply be a thing that is always on".
Now in some ways I might try to work with that concept with you if you were trying to improve aether currents but rather it just looks like you're removing the purpose they exist such that flying is available in any situation that it doesn't cause story concerns, and I don't think that is the right approach to content. The system exists for multiple reasons, and it might not do them all perfectly but it does have impact on them- I'd rather they're not removed so 'nothing' does what it used to do.
Naturally I disagree with pretty much everything you said about the system, especially since aether currents literally makes you deal with obstructions and scale of the zone else you /don't/ get flying. That not everyone might like it, being the thing I'd certainly go "certainly" to, but not everyone likes leveling up in an rpg too. I don't feel the argument to remove it, and what to replace it with, is good enough to do so. I might agree that they could mix the system up, but I don't think we'll agree for why for or the end result (like I might suggest making flying less strong overall, such as it has stamina or something and one must navigate the world rather than fly in straight lines like robots- perhaps best play tested in a specific zone like Eureka 3.0).