I don't know that I would ever say that Toy Story (the first one) or Bug's Life, or anything Dreamworks has done has a story remotely as well executed as The Incredibles. Even Shrek's reversal of the monster/hero isn't nearly as interesting as the hounded heroes in TI (and that's if you found Shrek interesting, which I would have been fine only seeing half of, no desire to see it again).
Incredibles was, as Skar said, self contained, yet remarkable well-informed and intelligent in it's awareness of it's context: both socially and literarily. The makers knew what informed their genre and story, and they acknowledged it at almost every turn, yet unlike even giants like TS Elliot, they did it without forcing you to read footnotes to understand it. If you'd never read a single comic book in your life, you could follow what was going on and get a lot of entertainment out of it. but if you'd read comics, esp the greats like major events in the Fantastic Four, The Flash, the X-Men, Superman, and the Watchmen, the more layers you get out of it.
And teh animation was more than appropriate. I'll agree that maybe it wasn't groundbreaking (I'm not an expert on animation technology, and I'll never pretend to be) but it was better executed than most any animation. Definitely easier on the eyes than the Final Fantasy movie (I'll admit, it may have a lot to do with the lack of scriptwriting in that one, but many of the visuals were downright confusing and misleading, and didn't contribute to involving me in the story or investing me in the outcome). The incredibles had the virtue of doing animation that didn't scream out that it was animation. Maybe that's not new technology, but it demonstrates a lot of skill with the medium.