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Before you hastily say 'no' and call me an idiot for bringing this up, let's talk this through.
Most people wouldn't consider it canon simply because they hate it, and that's understandable.
But let me talk about what NIMH 2 did right, and yes, it did do some things right (I'm serious):
~It focused more on the NIMH scientists.
Let's face it, the first movie portrayed NIMH as a cartoonishly dark and evil animal torture chamber. There were monkeys and dogs that were crying for some reason and even Nicodemus himself described it as being "put through the most unspeakable tortures!" The fact that NIMH is pretty much this evil castle in the sequel is not too far-fetched, IMHO. It might as well be for all we know.
But back on point, the scientists themselves are nameless in the first movie, which the sequel does in fact address. You could say they did it poorly, but refer back to the previous paragraph, the movie painted itself in a corner by making NIMH this cartoony torture chamber for animals. It's only natural for NIMH to be the antagonist here, unless we were doing a conflict between the Thorn Valley colony itself, but I feel (and this could be debated) that NIMH had to be involved somehow. Why? Because the film is called 'Secret of NIMH' NIMH didn't magically go away after the first movie, they're still a part of the universe.
~The lost mice.
I really like this idea of the mice from the ventilation shafts starting their own secret colony. Again, you could hate this aspect of the film and how it was done, but there's some creative effort here. It gives us motivation for our characters to go in to the NIMH labs themselves and save them. It gives us a setting change and a new perspective.
I also like the idea of one of the Brisby children siding with NIMH. Why? Because, IMHO, it allows for growth of the children from young scoundrels the first movie made them out to be into something greater. It could also create tension not only between Timothy and Martin, but Teresa and Cynthia (granted the sequel didn't bother with that, but we're thinking positive). It's only natural for the children to go their separate ways as adults, and keeping them in the story like this isn't really all that unreasonable.
.......Uh........not really...but it was funny!
Alright, alright, so my point is that while its status as canon is questionable, it did have some solid ideas that could make a case for it being canon. But yeah, probably not.