You know how most Layton games have some really dumb twist in them, one you try to overlook because the characters/development outside of the twist is enjoyable? Well this game has twelve dumb twists and no good characters or development.
The conclusion to the final case of the game is the stupidest thing in the series. I don't mean that in a 'wow, that was crazy,' way, but in a completely and utterly bafflingly stupid way. In the sense that the entire case would have never happened if a certain character had divulged a secret they had no reason to keep.
Oh, and they introduce a mystery in the very beginning of the game involving one of the main cast and then never solve it. They don't even not solve it, they actually never make any progress towards solving it at all. Then there's a 50 episode anime sequel where the 'what happened to Professor Layton?' question is given something like three whole episodes and is also stupid, but the weird kind of stupid the series is known for.