Best possible way they could have implemented flight. Well, they could have avoided linking aethers with out-of-the-way sidequests I suppose. But for the most part, it's the best way they could have done it.
If they let us fly right away, it would have been a huge waste. At least by making you explore the zone first, you experience everything.
It's fun... You go explore first, feel the land with the danger around. What so fun if you can fly straight away? Feel too easy if you can fly just like that, there is no difficulty on that and you can ignore all the mob with flying while questing.
Overall I liked it. It was fun trying to figure out ways to reach currents placed out of the way. The only mildly annoying thing was also having to receive some from quests since you had to stab around until you found them all or bite the bullet and rely on a guide.
I think of the aether currents as lore explaining why seemingly unwieldy creatures can take to the air..."Fat Chocobo" I am looking at you.