The worst thing about Skyward Sword is the missed potential with the Sky realm. It sure would have been nice to explore it more, but oh well.
Also I know everyone ****s on it all the time, but I really liked the controls. It made almost every enemy encounter matter, you couldn't just smash your way through most of the game. I found all the controls except the "falling/skydiving" to be perfectly responsive, though I will concede that I looked like a massive dork playing it. Plus the boss battles were super awesome (with amazing music) and the puzzles were at least slightly difficult this time (I'm looking at you Twilight Princess). Plus I appreciate the fact they tried to do something different with the progression and over-all play of the game. Instead of a rehash of Ocarina of Time (I'm looking at you Twilight Princess).
However it does feel like they didn't do enough with the game to warrant it's long development, the art direction was lacking (In this aspect TP was better for once), and Fi was quite obnoxious. The lack of a decent overworld certainly is crappy, but I'd argue the last good overworld in any Zelda game was Wind Waker (well until ALBW). I just genuinely think that the combat/controls make up for most of the games shortcomings. To me, it felt good enough to give it a distinct and unique experience.
Though, with the hugely positive reception to A Link Between Worlds, I'm rather excited for Zelda's future. Though I hope Nintendo figures out what they did right, instead of focusing on the wrong things.
Edit: I think a massive Skyrim-esque overworld would be terrible in a Zelda game. Games with large overworlds tend to be very glitchy and mostly empty. If Zelda games like MM and ALBW have shown us anything, its that a smaller overworld is perfectly fine when filled with lots of things to explore. For example Twilight Princess had a massive overworld, that was mostly empty. Getting across it was annoying and uninteresting. If they shunk the size down and spent that extra time on filling it with things to find, or at least making it seem more "alive" It would have been a better game for it.