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.
The March Hare and the Dormouse, much like the first game, are built up to be early bosses as you search for Hatter's arms and legs, but the only thing of note they do is try to impede your progress in your quest. They both flee after you break their machinery and defeat all the enemies in their area. At the end of the chapter they prepare to fight her inside a Humongous Mecha, but are ejected from it when the Mad Hatter throws a big ol' teapot at it.
The Executioner chases you through the Queen of Hearts' castle and the now-rotting hedge maze, and is completely invincible... that is, until a cutscene kicks in where Alice finds and eats the cake that makes her grow much bigger in size. She simply stomps on the Executioner, who is now so scared he drops his scythe.
To be honest, the only realBoss Fight in the game is the final one against the Dollmaker on the Infernal Train.
Judging by the level design and concept arts there should be a boss battle at the end of each chapter. They're absent probably due to budget/deadline reasons.
Badass Decay: Literally. Last seen as a towering, shrieking 300-foot tall monstrosity spread across Wonderland, the Queen of Hearts is now trapped in her rotting kingdom, physically resembles Alice's older sister Lizzie (Alice's superego according to Mcgee), and besides Caterpillar is among the few helpful people in Wonderland.
Breather Level: Cardsbridge, the first level of chapter 4. No enemies, no disturbing imagery, just peaceful jumping puzzles as you wind your way towards a horrible rotting castle inhabited by your worst Wonderland enemy.
All of chapter 6, what little there is, is a breather after chapter 5. No enemies, no platforms, no secrets; there's literally nothing at all except the final battle and a few cutscenes to close off the plot.
Common Knowledge: Once again, this game merges the Queen of Hearts and the Red Queen into the same character, going so far as to include chess motifs in the design of the Queen of Hearts' castle.
Complete Monster: Big BadDr.Bumby is Alice's shrink who uses hypnosis in order to erase Alice's traumatic memories of her family's death. The reason being that he's the one who started the fire that burned down her house in an attempt to hide his tracks after raping Alice's sister Lizzie. Nowadays he makes a profit on the side via pimping the children he's brainwashed and broken into Empty Shells.
His Wonderland counterpart, The Dollmaker, is naturally just as bad, to the extent even the Big Bad of the first game despises him.
Demonic Spiders: Depends on the difficulty being played on. Once the 3x damage multiplier gets applied on Alice, the various enemies that usually connect hard hits frequently(and dodging from Alice's attacks quite often) will start to look like these.
Fridge Brilliance: The visual difference between Reality Alice and Wonderland Alice may initially be of how she chooses to perceive herself as, but in the case of her hair, once you've gone through the Madness Returns storybook prequel it reveals what happened to her hair anyway.
The reason the Big Bad manifests itself as a train; it's actually a train of thought, specifically the one Dr. Bumby's implanting in Alice's head to Mind Wipe her and turn her into his corrupt whore.
Why the Jabberwock isn't back for this game unlike the Queen? Because the Train made his presence useless, just like in the Queen's case.
Also, the Train is trying to destroy Alice's memories of the fire. As it represents her guilt about the fire, the Jabberwock might have been killed by the Train before the game began.
On this point, the Jabberwock is dead before the train is "built" in the Hatter's Domain, but the train's influence is felt before that, and the Mock Turtle went to sea before the game begins, but after the train replaced his. This may lead to another point of Fridge Brilliance: that the train was not spawned by something in Alice's mind.
In one of the first three trailers, Alice is talking to Dr. Bumby, and he says "Alice, tell me of your Wonderland." and then she opens her mouth and blood and teeth fall out. In dream interpretation, your teeth falling out indicate that the words you're saying should have stayed in your mouth.
The black sludge of the Ruined enemies and the Dollmaker could actually be coal of some sort: it can burn Alice, hardens in a brittle substance when the enemies are killed and it's related to trains... And it does take place in Industrial Revolution London.
It is hinted to be at least partially inspired by the flammable chemicals used in her father's photography, but it is more likely something a train would spew.
Game Breaker: The fully-upgraded Teapot Cannon. Shatters enemy defences with one hit, is able to kill them with another.
Goddamned Bats: Quite a few enemies may qualify, but especially the Bolterflies and Ink Wasps if they make contact.
Good Bad Bugs: This, which will in about twenty minutes get you an 80G achievement you'd normally have to replay the entire game for.
Harsher in Hindsight: The things the orphanage kids say to Alice during the first London segment come off as innocent, if a little odd, first time round. Then you look back on them with the knowledge of what Dr Bumby is using them for. One notable example is this conversation between two little boys- "She [Alice] hates being touched" "Who likes it, then?". They're being used as prostitutes. You do the math.
It Gets Better: The Foundry, which is only the second area you visit, is easily the dullest area of the game, and one of the longest. This led to many a bad review from people who didn't know it gets better after that.
Most Annoying Sound: "A good worker is a live worker! Paid to live and work! A bad worker, is a dead worker; and vice versa! Don't be a bad worker, bad workers are slaves! And dead! Payday for good workers has been suspended indefinitely! Payday for bad workers is CANCELED! A good worker is a live worker! Paid to live and work! A bad worker—"
Don't forget his other speeches.
Sidetracked by the Gold Saucer: Averted. The Radula rooms lock up after you complete the events. Not like they're particularly interesting or addictive anyway.
Some Anvils Need to Be Dropped: Children forced into being sex workers. This is a massive problem, especially in third world countries, that doesn't get much attention.
The Woobie: This game makes Alice look a lot more like one than the previous game. Also several other characters, some from the first game, are (still)this.
Uncanny Valley: Not just the wonderlanders, but if you really find those prostitutes in London attractive, you either have an awful taste in women or a REALLY frustrated Libido.