Although I love Zelda, I always felt the climax to the end of a 3D title was always just, flat. It's like you have all these cool weapons, you went through all these awesome dungeons, then you have nothing to use them on.
Sure a hookshot to a chest there, a bow and arrow to a skulltula there, but I felt as though they could never represent the giant playground that was represented in A Link to the Past. Every item you had pretty much had a role in the overworld. The Magic Hammer, the Canes, everything.
Ocarina of Time has a nice overworld, Majora's Mask is small but full of things to do, Wind Waker has sailing and treasure hunting, Twilight Princess is epic but empty and Skyward Sword's is dungeon like and spiraling, but they all just lack the feeling of "doing what you want to do".
I'm not trying to turn this into a "what game has the best overworld" post. I'm just saying Miyamoto/Aonuma's staff makes great items and great dungeons in 3D. They just need to find ways to make them work. It's like they're afraid of elevation in their level design or something.