From Avclub and io9.com:
The Secret Of NIMH leaves basically every kid who sees it with a lingering dread

I am guilty of showing this movie to my own students, so hopefully (fingers crossed) I didn't traumatize them too much.
(It doesn't seem like I did.  They've been asking me recently if we could see it again, or if there was a Secret of NIMH 2, they could watch, so it seems like they enjoyed it.)

The reviewer hits many of the main points about the movie in the article linked above, so I'll just add a couple thoughts of my own:

1) While I was creating PowerPoints for this movie, I used a lot of Screencaps to help break down the story and dialogue for my students (I used the ones available at this site here).
In the process of pouring over all these frames of animation, I noticed something.  The animation on this movie is absolutely stunning.
Not only lots of detail in the frames, but also very interesting perspectives and camera angles.
This was Don Bluth's first animated feature after he broke away from Disney, and it's apparent that he was out to dazzle the world with his first movie.
It's a pity it never did well in theaters, but I suppose it has done well enough on home video to cement Don Bluth's reputation.

2) As the reviewer says (in the article linked to above) the main plot for The Rats of Nimh is relatively straightforward, but all the backstory and side characters make it convoluted.
Too convoluted, says Roger Ebert.  " It is not quite such a success on the emotional level, however, because it has so many characters and involves them in so many different problems that there's nobody for the kids in the audience to strongly identify with."
It never bothered me as a kid, but as an adult, watching this movie with my students last year, I noticed it.  There's too much story crammed in here for any of the characters to have meaningful arcs.  There's a lot of complexity hinted at with with the backstory of the rats of NIMH, but it's never really fleshed out.
The book on which The Secret of Nimh is based, Mrs. Frisby and the Rats of NIMH, is much better.  Or at least, it is if memory serves.  (The last time I read the book was all the way back in 5th grade.  But it made an impression on me, and I can still remember many parts of it clearly.)