You're not missing a ton. Atlantis isn't terrible, but it's definitely among Disney's periodic nadirs. I put it on in the background one night maybe a year ago and it didn't really hold anyone's attention. Someone on this page complained that Aladdin's CGI elements have aged poorly, but I really think people rewatching late-90s/early-00s Disney will find it even worse. The CGI-2d blending isn't great, I don't really like how... chunky the characters are. But basically I think the film doesn't work because it tries to be an Indiana Jones or Romancing the Stone, and I don't think anyone had it in them. So you get none of the classic Disney musical formula, and you get just a kind of lame action cartoon. Honestly, Aladdin III hits some of the same adventure vibes, only better... well, at least that's my memory, I last saw Aladdin III on VHS. The characters aren't really engaging. It's just kind of dull.
That being said, obviously as with any Disney movie if you haven't seen it, give it a watch. I'm just saying I wouldn't have the expectations that it's a lost gem.
Emperor's New Groove, by contrast, is one of Disney's most creative films.