A slight chunk of what took so long is that Brad moved on to live action films. The last Mission: Impossible and the upcoming Tomorrowland, specifically. Glad to see him return to Pixar.
I completely agree that out of all the movies, Incredibles solidly deserved a sequel over the other Pixar films, but also agree it isn't something to be rushed into. How do you follow up a movie deconstructing classic era style super heroes? That was the big question. There were some nice stories in the Boom comic book series, but I don't think there was much that could have gone through a 90 minute movie. Brad only wanted a sequel if they had the right story to tell. Considering that Disney could have very well made a cheap, less meaningful sequel if they didn't buy Pixar, I don't mind the wait.