Lack of plausibility
In most part of the movie it looked like just another cartoon with humanoid animals.
Then it explains that rats became intelligent from some evil scientists work. So, should I imply that rats can talk, read and use machines because they were changed? The cat in example never talks.
But if so, how can the crow and the owl talk? And how can they use magic?
And how come they just woke up some day and figured they could read text, without ever having learned it? I mean, ok, it's plausible that some mental health experiment makes animals smarter, but they'd still need to learn stuff to know it.
I understand the movie is based on a book and NIMH is important in that book. But in the movie, NIMH has little importance. It'd be better to just take away NIMH, its secret and the explanation for why there are smart rats and just let it be another fantasy humanoid animals cartoon.