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: The second phase of the final boss almost never attacks you and does piddling damage when he does. It doesn't help that the Chancellor Cole fight immediately before was both harder and much scarier.
Broken Base: The train. What's interesting about it is that fans tend to like it or dislike it depending on their view of how the franchise should be:
People who like Zelda games for their puzzle solving, combat and story tend to be OK with it. They consider it brings some fresh air to the series, especially regarding atmosphere, and that it fits in a handheld game.
People who like Zelda games for their sense of exploration and discovery are the ones who tend to hate it, since they think it utterly kills both characteristics without leaving a trace.
Dark Trains. They're invincible, and hunt you mercilessly on the tracks. Heaven help you if you're sandwiched between two of them on the rails. Why? Because they kill you in a single touch! You can slow them down temporarily with five cannon strikes (useful if you're reduced to reverse-running from one), but if you attempt to do so, watch out for the other one circling behind you. Then there's the armored versions of them. Same one-hit-kill if you run into them, but they'll actively pursue you, going so far as to turn around on the track to continue chasing you should you manage to fake them out, and unlike their unarmored cousins, can only be slowed down very slightly with each hit. You finally get to kill those bastards in The Very Definitely Final Dungeon. And it's so sweet to see them destroyed by you running through them.
Freud Was Right: Anyone else feel something with the very end? Namely that Link drives his sword (an ever popular symbol for this trope) into the Big Bad's head, and then you must rub the screen. Zelda then comes along to help, er, rub Link's sword. Then when the sword actually pierces the boss' skull they give out a rather... ecstatic cry.
Holy Shit Quotient: The Final Battle, one of the most epic in the entire franchise, filled with moments that almost sent a lot of fans into a joy seizure.
Memetic Mutation: While at first, several topics used the pre-existing "This topic sucks and is now about trains" meme to discuss the game, it soon became known as "Soul Train" over several boards.
Ever since the last trailer, the new meme seems to be "The Phantom wears a dress."
The Demon Train was also known at one point as the "Ganon-train" due to how similar it looked to cel-shaded Ganon. Of course, Ganon never appears in this game, but the name has still stuck.
Moe: Played for Laughs whenever Zelda possesses a Phantom. For the rest of the dungeon, you're followed around by half a ton of loudly clanking armor that recoils at mice, acknowledges your orders with adorable squeaking noises, and makes girly poses whenever you talk to her. Even the other Phantoms notice that she's "CUTER THAN USUAL".
Random Phantom Guardian (to Zelda): SOMETHING'S DIFFERENT ABOUT YOU TODAY.
Zelda's dialogue when you leave the Dark Ore Mine plays it straight.
Nightmare Retardant: While most players agree that Malladus in Zelda's body looks creepy as hell, his look outside of possession is more likely to make you laugh than scared, with those goofy-looking teeth.
The Lokomo songs can be annoyingly touchy, both in requirements and in controls (the mic seems to make a lot of double notes from a single blow, and it's a real pain in the ass to hit two notes not next to each other without hitting any of the ones in between). Not to mention the fact that relying on the microphone makes them simply impossible in places with a lot ambient noise, such as on a train or airplane, or in a public setting... in other words, places you would want to use a portable system.
Some people have noted that Phantom Zelda's AI has certain weaknesses that can make controlling her and Link in tandem a rather annoying task, especially in midboss and boss fights.
The warp gates, which are made so complicated that it's almost pointless to use them.
That One Boss: Fraaz. He's surprisingly hard for being only the second boss in the game, and he's the most Dangerously Genre Savvy enemy in the game to boot; his main form will aim where the game "thinks" you'll be when his shots reach you - he's the only non-overworld boss in this game to do this accurately - and after the first form cycle, he'll destroy the torches you were using against him. (Phytops will also try to "lead its target" with its goo shots in some parts of its fight but, unlike Fraaz, if you keep moving in the same direction Phytops will usually miss.)
The three-part final boss requires some crazy nimble reflexes with your stylus, likely enough to induce arthritis. This applies to the Chancellor Cole fight, guiding Zelda up to Malladus while destroying Cole's magic mice, and batting away Malladus' fireballs while Zelda charges her magic. Thankfully, the final scrap with Malladus proper is easier.
The final floors of the Tower of Spirits are the most devious part in the game, since they're packed with a vast array of puzzles, hazards and passageways that can only be tackled by out-of-the-box methods that make use of all of the items in the inventory and clever cooperation with the various types of Phantoms Zelda can possess. At one point, Link and Zelda also have to find three keys to access three different rooms whose puzzles can only be solved when all of those rooms are available for access. Near the end, there's also an invasion of several powerful enemies (including three high-tier Geozards) where Link must triumph while avoiding a pitfall.
That One Puzzle: The door to open the Ocean Sanctuary. Different in that it's not actually difficult to figure out, but the door won't accept the symbol you draw unless it's absolutely perfect.
That One Sidequest: The Dark Ore sidequest. You have to carry some ore that melts in sunlight halfway across the world map, and the only way to keep your cargo intact long enough is to go through a tunnel - inhabited by a Rocktite. Made tougher by the fact that you're also harassed by smaller ones. And getting hit causes you to lose some precious ore, so the bottom line is that you have to fight one of the tougher bosses in the game and take no more than one hit. There is a bit of a Guide Dang It cheat, though... The boss appears as soon as you enter it after unlocking the track, but only in the direction you need to take with the ore. You can beat it, then go pick up some ore and deliver it at your leisure, since the Rocktite won't ever respawn until you save and quit (the smaller enemies do, but they aren't as bothersome without the big one to focus on).
Toy Ship: Even some fans who are diametrically opposed to shipping Link/Zelda will acknowledge the adorability of their bond in this game.