Bad Export for You: Not bad, per se, but the US version is very obviously an unmodified port of the British localization, down to the last "metre", "defence", and "Your Honour"—nothing outright detrimental to the gameplay, but still highly noticeable. It also keeps the British voice actors for Phoenix and Luke despite both characters having American voice actors in previous dubs. This is especially baffling considering the 5-month gap between the two releases.
Different designs for most other characters, including a much more youthful Storyteller.
The whole "how could you have known what's in a book you never read" element. The concept of the book containing the entire past, present, and future history of Labyrinthia exists, but isn't used in that way.
The revelation that Layton is Phoenix with his Butt Monkey tendencies removed was just begging for Maya to go into fangirl mode Squeeing about how cool he is, comparing the two of them and generally getting under Phoenix's skin about it (because she's good at that). But...nope. There's a brief time or two where Phoenix gets annoyed because he feels a little useless next to the resident Spotlight-Stealing Squad, but it's nothing near what it could have been.
The famous Phoenix on a horse◊ art is never seen in game. It is given a small nod, though: when you examine the horses out in the forest, Maya wants to know what it will take to get Phoenix on one, no matter what!