It gets flak due to being unfinished (which is what the article is about). The movie itself jokes about it being unfinished a few times. It was also the first film released after Tarzan, which many say was the end of the 90s Disney Renaissance, so it was a tough act to follow and a tonal shift.
After Emperor's, we got mediocre films - with Lilo & Stitch being the only exception. Many consider Emperor's to be the first of this run.