These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anticlimax Boss: Argorok. He's after one of the most challenging dungeons in the game. And he's a giant dragon you fight on top of the City in the Sky during the middle of a big storm. Despite the absolutely breathtaking setting and circumstances, he goes down with very little fight in a rather simple boss fight, to the point that many players will switch back to the Ordon Sword just to drag the fight out a little longer.
Breather Boss: Morpheel. The fight is sandwiched between a very frustrating dungeon and the emotional/plotline climax of the first half of the game. If anything, the fight is more finnicky than hard. In fact, you have to really try in order to take damage from the second form, despite the fact that if the game actually obeyed the laws of physics, Link would probably die quickly just from the pressure waves caused by something that huge swimming around.
Armogohma. The first phase of the battle is incredibly straightforward and the second phase is literally a joke. As with Morpheel, you really have to try in order to get hurt in this fight.
Breather Level: The entire second half of the game after the lost woods. With no more Twilight realms, the ability to transform into a wolf at will, and the fact that you've grown stronger at a much faster rate than your adversaries, life is good.
Is a realistic style the 'correct' look and appearance for a colorful fantasy game such as Zelda? Many were divided. Some loved being able to see the world of Zelda, warts and all. Though others find those details less appealing at times (read: the Gorons)
One that is debated among both detractors and fans is Ganondorf's inclusion. It is either one of the series' greatest Boss Battles or an unnecessary addition which undermines Zant's character.
Contested Sequel: To Ocarina of TimeandWind Waker. Considering both this and the latter are very different, and this and the former are quite similar, disputes over this game predictably end up contested by either party.
Demonic Spiders: The ReDeads in this game are some of the hardest enemies to deal with, since if you get in certain range of it, it instantly does its infamous shriek leaving you defenseless, then hit you with its BFS, which takes off a big portion of your health.
Ilia. Link/Zelda and Link/Midna shippers blow her overreaction to Epona's minor injury out of proportion until she is a complete Jerkass, even though Ilia herself admitted she overreacted and apologized to Link for it.
There's some, but not quite as much, of this toward Zelda. Generally though, the more mature Link/Zelda and Link/Midna shippers tend to get along.
Like with Zelda, Midna gets this too from some Link/Zelda shippers, it doesn't help them that Midna spends most of the time interacting with Link.
Mortal Draw. It takes a little practice, but is by no means difficult — if you can perfect re-sheathing your sword mid-battle, you can oneshot any regular enemy, and kill bosses in three or four hits. And you can get it about midway through the game.
Ooccoo within the dungeons. There is a trick that if you warp out of the dungeon and then save, you can go back to the exact same spot you warped from after saving. This is especially useful if you're short on time and don't want to go all the way through the dungeon again.
It only works in the second dungeon, but switching out the boots just before landing on a magnetized surface allows you to walk at normal speed across the ceiling (putting them back on and off to drop). You can't roll or use items, but it is a lot faster (and quieter).
There's also the glitch that allows you to use infinite bombs and arrows (and thus infinite bomb arrows) through exploiting the minigames on Zora's River.
Hell Is That Noise: You can tell that hand in the Twilight Realm is gaining on you when you can hear that horrifying noise. The Twilight leitmotif in general.
Hype Backlash: Inevitable but when released, Twilight Princess was praised by fans and critics alike for being a return to form after the more experimental Wind Waker. Years down the line though have caused a reverse of opinion, with Wind Waker getting more praised for it's originality while Twilight Princess now gets derided for being too similar to Ocarina of Time, too linear for a Zelda game, and too brown.
Those on the "They changed it" side complain that Twilight Princess is not 'Zelda' enough due to being somewhat linear in comparison, especially towards the beginning where it has to open the sandbox.
Les Yay: Midna and Zelda exchange plenty of meaningful dialogue and looks and are very motivated in helping one another, to the point of Heroic Sacrifice. Midna often gives Zelda a grin. Also a little questionable is that Midna call Zelda 'Twilight Princess' when that's her title. How do you think she could also be called that?
Memetic Mutation: Just as this was invoked in-universe, the Malo Mart dance also became a meme online — see here and here.
Zant mortally wounds Midna, who while still jerk had grown on the player by that point. You then have to carry her to Zelda as she begs you to hurry. When you reach Zelda, you learn it was so Zelda could help you not her. You then watch as Zelda sacrifices herself for Midna, despite her pleads not to.
Scrappy Mechanic: The way rupees are handled in this game irritate most players. If he doesn't have space for a rupee you find in a chest, Link puts it back in the chest. Since the game practically hands Link rupees, he'll run into this often, leaving a lot of dungeons from being 100% cleared until Link empties his wallet. Moreover, every time players start up the game, it will always remind them how much differently-colored rupees cost... even the blue and yellow ones.
The fandom has tons of it for this game, especially since (except for the ones listed under Happily Married) there are no Official Couples. The Link/Midna shippers equal, if not outnumber, the Link/Zelda shippers. Of course, then there's the Link/Zelda/Midna threesome option. And then of course there's Ilia to factor in to the equation....
Shad's also very popular with the shippers, being the only other Bishōnen in the game. He's paired with both Zelda and Midna as often as Link, and also with fellow La Résistance member Ashei. Yaoi fans also enjoy slashing him with Link.
That One Level: The Lost Woods. A twisting labyrinth of samey-looking chambers and passageways where you have to chase after the Skull Kid while fending off the endless Deku Puppets he summons. The first time you're forced to get through it as a wolf and the second time the Skull Kid isn't carrying a lantern, requiring you to track him down by sound alone.
Beating Yeta in a sled race. The first race, against Yeto, is fairly easy, as long as you're careful. The race against Yeta is more difficult in comparison. To beat her, you have to take the high-up shortcut, which A) has a very small entrance point, and if you miss it you'll smack into the wall and thus never, never catch up and beat Yeta; and 'B) takes extreme precision to avoid falling off the edge. And though easing up on the control stick can make it easier to control yourself and thus avoid sailing over the edge, that's not an option here, as you won't beat Yeta to the finish line unless you go full-speed the whole way.
Bringing a barrel of spring water across Hyrule Field. Not only is the barrel a One Hitpoint Wonder that doesn't survive being hit by enemies or thrown, the enemies are Giant Fliers (who flap in very close, making it difficult to see what's going on), plants (who circle around you in ever-tighter circles), and Bulbins (who shoot your barrel full of arrows). And to top it all off, it's a Timed Mission, killing all enemies before moving on only ensures the water cools down and therefore useless. Fortunately, you get a piece of heart out of it.
Collecting all 60 Poe souls. They only appear at night in the only 3D Zelda game where you have no control over night and day, and it ultimately leads to a Bragging Rights Reward.
Uncanny Valley: Ooccoo, who is basically a chicken with a human head. Much more unsettling than it sounds. Her son, Ooccoo Jr., who is a child's disembodied head with wings on the sides, is even worse.
Zant. During the boss battle with him, and the scene immediately before, he twists into various unnatural positions, and makes some very odd high-pitched noises. He is possibly even more creepy-looking when he's not wearing his huge robe and helmet, due to his creepy eyes and proportions being easier to see.
Midna's true form is certainly quite beautiful, but hearing that same childish voice coming out of that Amazon body? REALLY unsettling.
The Twili in the outside portion Palace of Twilight dungeon both before and after you change them back with the Sols (with the exception of the little kid Twili). Before, they look like oddly shaped Shadow Beasts, but they don't attack you. They just stand there. And it doesn't stop when you change them back as like before, they don't attack you. They just stand there. It doesn't help that you can't even talk to them and every time you pass by them, they make that weird moaning noise.
Vindicated by History: There was a time after this game came out where it became socially acceptable not only to like Wind Waker, but to start comparing it to Twilight Princess favorably. Once Skyward Sword came out, suddenly the same happened to this game. By the time the next Zelda game is released, everybody will probably lighten up to Skyward Sword too.