Why did they change the fire temple music?
Why is the textures in the spirit temple diffrent in the GameCube version?
Why didn't they fix the previous bugs from 1.2 into 1.3's (GameCube) release?
Why is the Water Temple eaiser in the Master Quest?
Oh, I saw that it looks too much like the Turkish flag. But the big mystery to me is the first one. Did they think it was too creepy? Didn't sound so bad to me.
Technically speaking it is shorter but the puzzles can be a bit more difficult. Of course if you are using a walkthrough for this game then shorter=easier since no puzzle solving is involved. The reason it's shorter is that you only have to go through certain sections if you are collecting Skulltullas. I guess N wanted to give people a break after getting this far.