The quality of the music in Skyward Sword was amazing. My ears were happy campers when I was playing that game.
Still, there weren't that many super memorable pieces that I could hum off the top of my head. It was mostly atmospheric tracks, which have their place in any game, but sometimes you want areas to have a distinct catchy tune playing in the background. So even though the sound quality was better from a technical point of view, I still prefer the soundtracks from Ocarina of Time and Wind Waker. Then again, the Dragon Roost Island theme alone pretty much trounces every song in every video game ever made combined. It's definitely a tough act to follow.
I'm not saying that orchestrated music isn't better than MIDI music. As LittleGumball said, nothing can beat the expressive sound of real instruments. I'm also certainly not going to bash Skyward Sword for its music. Overall, I would say it was really good, and some tracks stood out as exceptional. The theme for Faron Woods was enjoyable to listen to and the Earth Temple's theme had a good flavor and beat to it. "
Staff Roll" was a really good piece as well, with a nice mix of epic and serene moments.