All other Disney films have been failures because the stories all sucked. It really had nothing to do with the animation. The animation looked fantastic, but the stories totally blew.
Disney wasn't just the release studio on several Pixar films. They were the release studio for ALL Pixar films. Now they're another division of Disney. That alone should make future Disney films much more successful. I for one would go out of my way to see Pixar films before. Now that they're owned by Disney, they'll just get a bigger cut of the receipts.
I don't know how you can even compare any of Pixar's movies to Pokemon. The former are expressly designed for kids and adults alike with wonderful stories and great animation (whether you like the animation or not doesn't mean it's not great animation). The latter is a show strictly for kids that has only slightly more plot than an average episode of Dragonball.
And while Shrek 3 may not have been as good as Shrek 1 or even 2, it was still a fun, enjoyable movie. I really like the way those guys poke fun and make references to all the fairy tales.
So by your reasoning, all animation that targets kids is crap. Well, IMHO, Chicken Run was a pretty lame movie and Wallace and Gromit didn't look that good either.