I disliked that there was essentially only 4 areas, and no connection between any of them, besides the sky area. You least that feeling of adventure you get when you go to Lake Hylia, Zora River, The Lost Woods, the snow mountain from TP, Zora's Domain, etc etc for the first time. I know Majora's Mask also had 4 areas 5 or 6 areas, but they were environments we hadn't seen in a 3D Zelda, and all the areas had a lot of character and atmosphere, something missing from SS.
Also the puzzles outside of the temples was a little gruelling at times, I like exploring the world between dungeons, but when everything is a puzzle, it just sort of becomes tedious for me. The motion controls were alright, but I don't believe they improved the game in any significant way, and most of the music was good, the story and characters were awesome. Though, for a AAA game in 2011 (even if it was on Wii) it's kind of inexcusable to not have voice acting. Not saying Link should talk, but the NPCs should.
I liked the art style though!