Ass Pull: The rapid-fire revelations toward the end comes across as this. The fact that Layton has a brother (who is Descole), the fact that he was adopted, the fact that "Hershel" is not his original name, the fact that Bronev is his father, and the fact that Emmy is a mole for Targent are all twists with absolutely no foreshadowing or build-up.
The revelation that the Azran died out because of a robotic rebellion seems like just a setup to reveal Aurora as a golem so they can kill her off. That way, they don't have to explain away her character in the first trilogy.
The upgrade of the Azran from scattered Meso-American based culture with a penchant for crazy-ass architecture and before-their-time knowledge, to world-traveling grand race of super geniuses who could cure EVERY DISEASE EVER feels like the writers forgot how to explain plots.
Hilarious in Hindsight: One of the main characters is named Professor Sycamore. Guess who else is named this in Pokémon X and Y? It gets funnier when you consider that the Pokémon Sycamore's theme has a distinct Layton-like vibe to it. This becomes more hilarious if you played the previous game and related it to Pokémon Black 2 and White 2.
Inferred Holocaust / No Endor Holocaust: The golems, once activated, start blowing things up. It's a situation that is noted might be the end of the world if something isn't done. Yet the only sign of damage post-game is a piece of art during the credits depicting characters from Froenburg, who were specifically stated to have been evacuated prior to awakening of the golems, carrying building materials.
Moe: Aurora. Not only does she look very cute, whether in her Azran dress or her street clothes, but due to being a Fish Out of Temporal Water, her naivete and curiosity regarding even the most common things makes her even more adorable.
That One Sidequest: The fashion design minigame, which takes several cues from another series That One Sidequest, the tea brewing minigame from Diabolical Box, and as a result is every bit as reliant on trial and error over actually thinking it through to a solution as its predecessor.
Also, due to the order in which you get items, you'll almost inevitably end up finishing the first request last. It seems this minigame was specifically designed to be as irritating as humanly possible.
The Untwist: Did you watch the very first cutscene of The Last Specter? Then you should in no way be surprised that Sycamore is Descole, given the presence of Raymond the butler...
Woe be it to the fan who watched the American trailer. If so, You know Sycamore is, at the least, Layton's long-lost brother, due to the fact that the adoption scene is played almost in its entirety in the trailer.