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.
Fridge Brilliance: In Diabolical Box, there's a minigame which involves a hamster. The hamster speaks throughout the minigame, and also afterward, when he becomes the coin- and hidden puzzle-finding companion. This is a little jarring...then you remember that Luke is the one who is supposed to be interacting with the hamster, and Luke has the ability to communicate with animals. The hamster "talks" because Luke can understand him!
To put things into perspective, the first game was released in Europe nine months after its American release. Due to its success, subsequent games were always released around one month after the American release, with Miracle Mask taking a two-day lead in Europe and culminating in Azran Legacy coming out in Europe in 2013 and in America in 2014.
Ho Yay: Luke and the Professor seem a little too chummy the vast majority of the time, although it can easily just be read as a Bruce Wayne/Dick Grayson arrangement. Then again, that one has similar problems...
Somewhat lampshaded by Chelmey in Diabolical Box, who decides not to probe too deeply into the relationship.
The ridiculous amount of chemistry between Descole and Layton, as well. The former bends the latter back over a control panel in the movie.
Let us not forget Henry's motivations for creating Monte d'Or. Good LORD.
Nightmare Fuel: Don't let the cute and quirky character designs and whimsical settings fool you; all of the games have several examples.
Parents as People: Hershal Layton, as often joked about in the fan community. He's overprotective of Flora to the point of ignoring her on while on a case. It became somewhat of a running gag that Layton's so one-tracked minded on his adventures that he often forgets his adopted daughter. As for his son, Alfendi, he grows up to be a borderline-psycho Jerkass and Nightmare Fetishist. Luke on the other hand is brought along on his life-threatening journeys.
To be fair, we don't see Layton on his non-adventuring days very often, and Luke has proven himself to be, while absentminded, extremely competent and capable for his age.
Anthony: Oh, and if you get stuck, don't bother asking me for any hints. I'll provide nothing of the sort! I want you to solve this puzzle in its... purest form.
Luckily, by this point, the game has a memo function, which proves invaluable for planning the Knight moves before you try to put them into action. It actually makes life a bit easier.
The Chocolate Code in the English version of Curious Village. This one wouldn't be so bad if the translators hadn't changed the hints so that they didn't reference the most significant part of the clue's illustration.
One of the bonus puzzles in Diabolical Box asks you to multiply a three-digit number by a one-digit number to get a four-digit number using the numbers from 1-8 only once.
Ships That Pass In The Night: Flora and Clive. The ship potential is there, but they don't interact much unless you count Clive kidnapping Flora.
Randall being the Masked Gentleman in Miracle Mask. Mysterious figure wearing the mask that Randall had when he died, torturing the town that Randall's closest friend and ex-girlfriend, now seemingly WIFE of said friend are heads of, yells about the greed and corruption of the town, and they never found Randall's body? HM. I WONDER WHO HE IS?
And in Azran Legacy, it is pretty obvious that Desmond Sycamore really is Descole, at least when you played a previous game, as both have Raymond as an employee.
Spoiled by the Format: If several mysteries are not yet solved, you likely have a way to go, and you certainly do if not all of the mysteries have been found. Additionally, the number of puzzles for each game gives you some idea of how far you are when the number of a given puzzle appears.
They Changed It, Now It Sucks: Despite the fact that very little is known about it for now, Layton 7 is already starting to gain this reaction from fans due to basically being Professor Layton In Name Only. As in... in name only to the largest degree you can possibly get, to the point of being a non traditional puzzle game that doesn't star Layton, has a new art style and is made for both 3DS and smartphones.
The conversation Barton has with Luke in Unwound Future paints him as one.
Layton himself becomes one over the course of the series as more of his backstory is revealed. Unwound Future reveals the love of his life was blown up, Miracle Mask reveals his best childhood friend fell to his death and Layton couldn't save him, Azran Legacy reveals not only is Layton adopted and his real mother is dead, but his father and brother are criminal sociopaths, and Layton Brothers reveals his son is a violent asshole.