Flying on the loftwing was okay, though not my favorite method of transportation. There's nothing too wrong with it other than there's not much to it. I honestly felt more engaged sailing in WW or driving in ST, but that's just me. I think this difference stems in what you want to do while transporting. If you want to be engaged in your transportation, the loftwing method works well. If you want to be engaged in your environment, well then you won't find as much satisfaction, but that's really the sky's fault. Speaking of the sky, my feelings for it differ greatly. While I felt the loftwings were okay, I agree with you in that there wasn't much to the sky. Not many things to explore and the islands that actually held something worth exploring, you generally found them on the way to get a treasure, so it felt like they were meant to be found. It was lacking a great deal of enemies (which is understandable if you look at it from a story point of view) And because of how tedious traveling becomes in SS, the sky loses more points. How? I don't know, but it does. The music was grand for the first half of the game, but then got old and didn't feel like it fit anymore. And last, there is a lack of scenery to the sky, something other Zelda games have had in abundance. My main concerns with a 3D hub/overworld are secrets and scenery, both of which SS lacked moreso, imo, than any past Zelda game.
Thus, I was fine with the loftwings, nothing wrong. However, the sky was not my cup of tea and could've used serious improvement.