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, as you can slam the hammer in certain spots to distract Phantoms while you bolt off in another direction.
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.
The Scrappy: If you don't find Linebeck's over-the-top cowardice, greed, and pretentiousness funny, you're probably going to find it annoying. It doesn't help that you have to listen to him whine and rant every time you want to board the ship, in addition to his frequent cutscene appearances. He suddenly takes a few levels in badass and kindness at the very end, but this can feel like a bit of an Ass Pull and/or too little, too late after his ceaseless obnoxiousness throughout the rest of the game.
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 the dungeon is both timed and arbitrarily stealthy since you can't 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.