I just got a random thought. What if they implemented flying so that when you lift off, you go above the clouds where you'd have floating islands/continents to explore. They could even make it so that you can only ascend/descend in specific locations and explain it by there being dangerous levels of aether higher up in the air and there's a lower concentration of aether or a hole in the layer of aether in the locations where we are able to ascend/descend.
That way we'd still technically have flying, but without some of the negative side effects of flying, like people cherry-picking objectives and the world feeling less lively.
Just an idea and they'll probably never go for it, but I think it could be at least a little bit interesting.