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.
Foe Yay: Layton and Anton, when the latter's dialogue is taken the wrong way.
Anton: "It's been far too long since I've encountered prey so… feisty…"
Fridge Brilliance: Folsense is one letter away from "fool sense", and the way it's pronounced sounds like "false sense".
Fridge Logic: If Professor Layton and team were caught in the luxury car when it switched trains to go to Folsense, then where did their luggage go?
They evidently walk into town with them and have no reason to hallucinate them, either, so must actually be there; the real question is how did they get them?
Narm: The voice acting is at places very slightly awkward, but a more major one comes in the form of a Mood Whiplash. In the puzzle where Anton tells the Professor to choose a sword, a lot of tension is built up, which is all ruined by the Professor still doing his trademark finger-pointing, smile then catchphrase "success" routine. It is redeemed thanks to the ensuing Crowning Moment of Awesome.
Nightmare Fuel: The game's very premise involves a cursed object and a vampire subplot though both of those turn out to be false. Not to mention the dream sequence with the ball...
Not to mention the possibility of blood on the walls.
In fact, Anton himself is enough to scare the crap out of anyone.
Tear Jerker: The story of Anton and Sophia, especially her letter to him.
Anton and Katia's grandfather-granddaughter reunion at the end of the game. Even Anton and Beluga's reunion during the credits was touching.
That One Sidequest: The Tea Set sidequest. You have to make tea blends from ingredients you find throughout the game and serve specific blends to people when they are thirsty. This is annoying for three reasons:
First, coming up with the tea blends requires using 3 ingredients out of 8 (max 2 of any one ingredient). While several targets hint at the blend they'd like, narrowing your search down, the total search space is 504 potential recipes. This can be tedious and time-consuming without a guide.
Second, people have only a chance of being thirsty before you've satisfied them, some only a small chance. The randomness involved means that you will waste a good amount of time going back and forth in and out of an area to try to trigger thirst in a character. Also, some characters will be thirsty before you have the ingredients to satisfy them, getting in the way of a puzzle or clue from them.
Third, there's no list of who you've satisfied. So, unless you wrote it down or are scrupulously following a guide, there's no way to tell the difference between someone you've served and someone who just isn't thirsty yet if you don't remember who you've served tea to.
They do provide a counter at the top of how many people you've given tea too, however.
Shocking Swerve: Of course it's not a vampire, silly! That would be impossible. Instead, everyone has been hallucinating Folsense, with everything and everyone in it, this entire time. Because that makes so much more sense.
Viewer Gender Confusion: Anton looks more like Beluga's mother than Beluga's older brother. Where he is standing in the family portrait does not help.
Villain Decay: Don Paolo, the Big Bad of the previous game, was a genuine threat before. However, in this game his evil plot takes a backseat to Anton's story, and is thwarted in a rather more humorous manner than last time.
The Woobie: Anton in the final act. Also Flora, after Layton and Luke confront her about her disguise and she tells them she just didn't want to be alone again.