As shocking as this may be to hear, I don't really think The Secret of NIMH is all that great. Sure, it's beautifully animated, but it definitely has flaws. Jenner isn't really much of a villain (heck, he doesn't even show up until more than halfway through the movie), and Justin strikes me as a completely superfluous character - he literally does nothing of consequence throughout the whole story. He doesn't even get to defeat Jenner in their big swordfight at the end. Mrs. Brisby doesn't really do anything to save the day, either; instead, it's that Deus Ex Machina necklace that Nicodemus just happened to give her. And I'm sorry, I love Dom DeLouise as much as the next guy, but Jeremy is incredibly annoying.
I've seen the film twice now, and I still don't see why everyone says this is one of the greatest animated films of all time. I can think of at least 20 or more animated movies that have a more substantial story, stronger characters, and more overall entertainment value.