I'm still thinking about this. And really, I don't understand. What's so "layered" about the Toy Story movies or Monsters, Inc? they're all straight forward and predictable -- there's very little complex about any of them. What makes the Pixar movies so good is how they treat their subject. The toys don't act like people, they act like toys. The monsters don't act like humans, they act like people. The fish don't act like people, they act like fish. The supers don't act like accountants, they act like people would act if superhero vigilante was a real career.
In Bug's Life the Bugs... well, they don't really act like bugs. They act like people who have funny shapes.
I didn't like Cars for a plethora of reasons. Mostly because I'm supposed to have sympathy for the entire cast for the most pathetic of reasons. There's little reason to like most of them. The underlying elements were of little basic interest for me in the subject material, and the car elements are really superficial. There's conflict where no believable conflict exists.
It's not like I hate Bug's Life, but it's meh at best. and Cars is only a little bit better. Incredibles was very entertaining. And yeah, it's my favorite. But while your accusation that I only like Incredibles because it's about supers is at once unprovable and ... well, impossible the way you phrased it, I can acknowledge my prejudice. I enjoy watching Incredibles *much* more than either Toy Story, but I can, at the same time, realize that Toy Story was a better film. Still, Incredibles is pretty solid because of how it deals with its subject matter.