My criteria for a movie, animated or not, is the same. I have a raging hard-on for animation due to my opinion that animation is a far superior medium for storytelling than live-action. That is a whole other discussion, tho.
In my opinion, the most important element of a story are the characters. Characters are what makes the rest of the story happen if you've written your story correctly. The motivations of the characters and the clashing of the characters makes everything else in a movie happen. The movies I mention have, in my opinion, superior characters and relationships. Princess Mononoke is a really good film, I will admit, and deserves to be listed as one of the absolute best of the ghibli films and therefore as one of the best animated films of all time. Miyazaki's other movies are a bit more fluffy and loose with their characters and their motivations and actually lie to you about the motivations to a certain degree. You go through most of Spirited Away with a very negative portrayal of the villainess, but at the end of the movie I had a completely different opinion of her and she felt much less of a threat to me. I'm still not sure what her motivation was throughout the film, aside from just "I'm the bad guy, I have to make things hard for this girl". The girl was actually doing her huge favors for most of the movie, but the villain continued to harass her, neutered as she was by the end.
Mononoke is a great film, tho. I won't even try to argue. There's only one part that I think isn't utterly brilliant, and it's a stupid little trivial thing that no one in their right mind should care about.
The three films I mentioned are all extremely character-oriented stories, and I find that those films that emphasize character over plot end up with the most engrossing stories. Ghibli has always emphasized character more than most other studios - live action or animated - but I think Kondo and Takahata were/are better at it than Miyazaki. Not to say that Miyazaki isn't damn good at it - he is - but I would say those three films I mentioned are better than any of Miyazaki's films.
Just my opinion, tho.
Sorry for length, I'm a little drunk at the moment and it's making me possibly ramble more than usual - which is significant for a guy who tends to ramble even when he's not drunk.