The Great Mouse Detective is an awesome movie and it`s very underrated in my opinion.
Also Fidget is really underrated villain sidekick and Ratigan is underrated too.
Oh, wow. That's a hard question....
The Rescuers is seriously underrated, but at least people know about it.
I'd have to say Basil the Great Mouse Detective. It also has two different names. The origional is "Basil the Great Mouse Detective" but people changed it to "The Great Mouse Detective".
But I also think that The Hunchback of Notre Dame 2 is an underrated Disney movie. Sure the animation isn't the best, but it's one of my favourites, and people either don't know it or hate it. Plus, I think it's got the best Score