For me Skyward Sword was just marked by poor development choices clouding what would have otherwise been a very enjoyable experience.
The overworld felt basically empty. It's the area that you CAN explore but have no desire to explore. The ocean, while certainly with problems of its own, worked so much better just in the nature of the exploration and the characters that fill the world. You can basically ignore everybody in the sky if you want to. Sure, there are side quests, but after the opening sequence everybody that lives in the sky kind of just stops mattering. The characters throughout the ocean have their sidequests too, but even if you don't bother with the sidequests you still have some regular interaction with a lot of these characters in the main quest, and that actually draws you into the sidequests!
Then you have the ground below. Interesting and unique areas, filled with characters that I want to be memorable. These were areas that I WANTED to explore, but couldn't. This made the characters that lived there ultimately forgettable because they were nothing more than just part of the progression; you moved on past them after you were done in the area and there was no exploring the area around them that could teach you more about who they are. These are the characters that are actually progressing the storyline with you, and these are the characters you want to see developed more.
It's like, Groose is great, and then everybody else is just forgettable. I really can't think of any other character that sticks out in SS, and that's a first for me when it comes to Zelda games.
Don't even get me started about the Imprisoned...