The Incredibles is supposed to be Pixar's best film. It's not - Finding Nemo is. I don't recall being crazy about it when it came out, but having seen it about 200 times with my daughter since, it's almost perfect.
I agree with nearly all of your post except this. I'm not sure if you are implying that Nemo is underrated, but I
personally think it is overrated and have never understood why its sets the bar for Pixar movies for most people. Its good, but I think there are several better, including The Incredibles. At risk of hijacking this thread with a somewhat divergent topic, if I were to rate Pixar movies, they would be.
1) The Incredibles (The most rewatchable Pixar movie IMHO. Love the family interaction/humor and action which rivals any live action movie. And you have to watch Jack Jack Attacks! short as part of it!)
2) Wall-E (Wasn't originally sure about this one when it first came out and with practically no dialogue through two-thirds of the movie, but amazing the way they made you emotionally connect with a robot trash compactor)
3) Toy Story 3 (Any movie that can make grown men cry over stuffed animal and toys must be brilliant)
4) Ratatouille (Wasn't sure about this one at first either. I could not figure out how it could be any good, I was wrong. Just a solid, well told, and entertaining story.)
5) Toy Story (the original, nuff said)
6) Monsters, Inc. (overall story and movie was OK, but Billy Crystal and John Goodman totally sold it.)
7) Toy Story 2 (yeah, Jesse's song could make grown men cry too, but although a good movie, just not as good or memorable of a story as the other two.)
8) Monsters University (kind of a lame story, but funny. Billy Crystal and John Goodman still did good things with it.)
9) Finding Nemo (Love Dory and Crush, but I found the movie a bit slow and sappy. Not a bad movie by any means, but think other Pixar movies are better).
10) Up (very touching first act of the movie, and Dug is pretty funny - SQUIRREL! - but the story never pulled me in)
11) A Bugs Life (I agree that it is underrated, and still pretty groundbreaking early movie for Pixar, but their subsequent movies just got better and better).
12) Brave (I really wanted to like this movie more than I did. Not a bad movie, but it tried to be emotional, epic, and funny, and never totally sold it on any point)
13) Cars (I enjoyed it when I first saw it, but never cared about rewatching it. Not really bad or anything, but its probably one of the shallowest Pixar movies. Maybe Cars 2 drags it down my list further than it deserves.)
14) Cars 2 (just felt like a cash grab from toddler boys and a tie in for Cars Land at DL. The only Pixar Movie I would say wasn't really a good movie.)