Teran, allow me to correct you.
Uematsu did not arrange any themes in Brawl: all he did in Brawl was the Main Theme's composition.
The song arrangements were made by the 38 composers Sakurai hired, which you can check on
this Dojo post.
You can check who did each arrangement in Brawl's Sound Test feature, also available on
this Dojo page.
If you want to blame someone, blame the arranger behind the Brawl version.
Then again, I don't think the Brawl arrangements were that bad as some people say. In fact, I enjoyed most of the remixes. I could even say that some remixes surpassed the original versions.
All of this is my opinion, though, and therefore subjective, so let's not start an argument over this...
To stay on topic, my favorite Zelda is Wind Waker. It was my first Zelda game, so it has more nostalgic feel than any other game. Other favorites are Ocarina of Time, Majora's Mask and Skyward Sword. I also enjoyed Four Swords Adventures a lot, thanks to its focus on multiplayer.
I have to say that Skyward Sword is my second favorite, because of the story, that while not very deep, it was emotional. The soundtrack was very good and so was the ending.