What do you mean by "the usual rules?" Like, it contains many of the elements from the games but makes an attempt to create a storyline that ends by being completely unlike the original idea? I don't know. The only animated movie I've seen based on a video game was the Animal Crossing movie, and it followed the direction of AC:WW quite well, in my opinion. For example, the concepts of working for Tom Nook, moving in, other residents moving out, were all worked into the storyline in a way that felt natural.
However, I've never played Professor Layton (I plan to at some point) so I wouldn't be able to tell what are based from the game or not.