We should also throw Aardman into the mix of the great modern animation studios, thanks to them and Tim Burton stop-motion has been greatly advanced and found some mainstream traction.
I think early Pixar was great family entertainment, harkening back to Walt Disney's formula of heart, and humor that would keep children entertained and touch adults as well. They are also the pioneers of an entire art form the way he was with feature length traditional animation. Their scientists and artists are the reasons why many of the things that are possible with CGI exist today. Their technical prowess is reflected in the sophistication that blows every other CGI studio out of the water, and really started to be evident in Finding Nemo. Later on they started to gamble more and be much more mature while spending the mouse house's money and managed to still keep their box office numbers ridiculously high. Ratatouille is a big budget film that other than featuring talking animals is not at all oriented towards children, yet they pulled it off. Wall-E managed to sell a nearly dialog free movie to ADD children and their parents, though honestly neither demographic is among those who praised it so highly. Then they brought in Roger Deakins to try and lend Wall-E a more cinematic quality than previously envisioned in the genre, and lo and behold the first time DreamWorks makes a stunning CGI feature (How to Train Your Dragon) they hired the same man. Wall-E also carried with it an environmentalist message without shoving it down your throat the way Happy Feet did. Up has more broken-family tragedy in it than Walt's movies put together, but goes on to not only tell a fantastic adventure story but create a very restrained life-lesson story amongst that mayhem. And Toy Story 3 managed to be a hybrid of both early Pixar and adult-oriented Pixar.
These are legitimate achievements, no matter if their films are to your taste or what else is going on in the film industry. Cars 2 aside, any film fan has to be happy that some people with this kind of heart, technical skill and creativity have a ton of cache in a typically vapid Hollywood. Last bastion of animation? Obviously not, but that doesn't negate what they are.
It's like indie hipsters whining that people go on and on about the awesomeness of mainstream music and ignore the latest and greatest Pitchfork-approved album-- just because there are under-recognized artists out there doesn't take away their achievements nor does it mean that there can't be good things in the mainstream as well. There's room for both, one kind just happens to be more marketable than the other. I'm saying that I'm happy that one such group has found a fairly amicable partnership with a behemoth like Disney.
Also, let me remind you that Miyazaki won the Oscar for Best Animated Feature before any Pixar film did. If his films also managed to be box office smashes in the United States would we even be having this conversation?