Game Breaker: The Hammer. It's the first instance in the series of the hammer being a long-range weapon, as your Exposition Fairy will be the one wielding it instead of you, meaning you can keep your distance against certain enemies while you command your fairy to whale on them with it. It can even come in handy in the Temple of the Ocean King, for you can slam the hammer in certain spots to distract Phantoms to go off in one direction while you bolt off in the other.
It's Easy, so It Sucks: If a critic isn't harping on Temple of the Ocean King, chances are they're grumbling about this. Sandwiched between Wind Waker and Spirit Tracks, this game just didn't have any teeth.
Scrappy Mechanic: Returning to the Temple of the Ocean King. See That One Level below for details, but long story short: after every dungeon, you have to trudge to the same dungeon, do the same puzzles again, and by the way the dungeon is both timed and arbitrarily stealthy since you can't really hurt the enemies.
That One Level: The Temple of the Ocean King is one of the franchise's most hated, thanks to the repeat visits through the same rooms, the timer, and the ability of the Phantoms to knock you back to a room's entrance while reducing the time you have left. The Tower of Spirits was designed with the intent of remedying these complaints.
That One Sidequest: Getting all of the Heart Containers is hard work, especially given the difficulty of the archery minigame and Maze Island in general.