Better atmopshere and sidequests.
You can't have "two of the dungeons" and "water dungeon" as separate complaints.
I don't find the songs any more useless than in OoT, and I didn't find recollecting items to be tedious since you keep all your important ones. I liked the time limit and had no problem with the save system...hell I actually prefer its save system since you can start back up at multiple places.
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