All of what the OP said, plus:

Day/Night System: It could have been perfectly incorporated in the game. Link and his Loftwing could receive the according flashlight hats via sidequests so that Link could use his Loftwing anytime. The system could also have applied for the world below, making the world feel more alive.

More stuff to fight in the Sky: The Levias fight was executed in an awesome way, so I see no reason (except for the Sky meaning to be peaceful, hence the Goddess sending the people there) to not add more monsters in the Sky. I mean, it already had some worthless ones. Either have variety or none.

Overworld's Design: Don't get me wrong; I loved running through and exploring the world below. The only thing is that it seemed too made-up to me. Like a huge playground designed specifically for Link to traverse.

Segmentation: It was a nice change of pace to have a hub and go to several areas, but I much prefer the Ocarina Of Time and Twilight Princess way: actually feeling you're traversing a land, not segmented, made-up places.

With the above being said, I absolutely loved the game. By far one of my all time favorites. It's just that there are so many eye-pokingly obvious stuff they could have easily done with it but they didn't that somewhat annoys me.