For what it's worth, I loved Skyward Sword. I loved the controls, I loved that the overworld was a giant puzzle waiting to be solved. I shared the same frustrations that everyone else did, though. I found the controls a burden sometimes, and I definitely missed feeling like there were things to see and do in the game besides advancing to the next dungeon.
But what I found particularly odd about Skyward Sword, seeing how it's the first chronological title in a series that's so heavily rooted in medieval themes, is how mechanical the game felt -- especially when traveling into the past. That's when I started wondering if Zelda's actually set hundreds or thousands of years in the future.
Let's get this out of the way and admit that this is just a video game, and the developers are really just letting their creative wings spread unburdened by the logic of the first game in the series featuring technology far advanced compared to later entries. The team at Nintendo wanted to make Link travel back in time to a bunch of weird, robot Furbies with super-cool technology, which is set even farther back than the first game in the timeline. Now that's out of the way, let's get down to business.
So, what I've been thinking about is that just maybe the games are set far passed modern time, where science has advanced far enough to create strange, light powered mine carts in some creepy, super race of man-rodents. During this period, something cataclysmic inevitably happens and sends mankind (and Zora/Goron, etc) back into the stone ages we remember from games like Ocarina and Link to the Past. It isn't until Twilight Princess, which is one of the very last titles in the timeline, that we finally start seeing weird gadgets, like that chicken-mech-cannon that shoots Link into the Sky Temple -- and when society has rebuilt its wherewithal in the tech world. When I'm wondering why the tech in Skyward Sword surpasses that of later entries in the series, it seems like the only explanation is that it happened far in the future and saw the world crumble in on itself, only to have to start over and provide the medieval world we've grown to know in Zelda games.
Other theories are welcome, of course.