Skyward Sword was one heck of an adventure for me on my first playthrough. Everything about the game was made of gold (metaphorically speaking): the story, the combat, the motion controls, the dungeon design. Have subsequent playthroughs somewhat lowered my stance on it being a "perfect" game? Yeah. Do I acknowledge it's flawed in multiple areas? Yeah, I do. It's still an incredible game on numerous levels, and while it did commit some puzzling mistakes, it also introduced several awesome ideas (like money sinks and the stamina meter) that I'd like to see repeated. Even most of the people who don't like Skyward Sword usually hold it accountable for not feeling like a Zelda game to them (or what a Zelda game should be like), not because it's a bad game in and of itself.
Congratulations on your conquering of Skyward Sword. Now go and kick some more butt in some more Zelda games.