You do bring up an interesting point. However there is one part in "The Muppets that I personally fill is out of character of Gonzo. From his very first appearance on the Muppet Show everyone including Gonzo himself knew he was a weirdo.In fact as the show and movies came out he was more and more confident, and proud to be a weirdo. I don't think he would ever hide that, or ever say no to the chance to being a weirdo on stage. Other then that one thing Gonzo was spot on back to his weirdo self in both movies.
Personally, I think they should have traveled to Bombay, India to pick up Gonzo. Imagine an epic Bollywood number that would have made!
As much as I appreciate Segel's success with bringing the Muppets back to mainstream audiences, I can't help but feel he was much more of a casual fan who didn't quite get what made them tick. He also skewed more mid-80's retro when the bulk of the Muppets' retroness belongs in the late 70's to early 80's. Nonetheless, an enjoyable film.
Oh, and as for Gonzo's absence. Dave Goelz is the elder Muppeteer these days. Gonzo's not gone, but I think he's letting the younger talent pick up a little more of the slack. That's all this is. Remember back to Muppets Tonight? Gonzo (along with Rizzo) really took on the backstage roles of Kermit, Scooter and Fozzie. There was a lot of him on the program. After the recasts, Scooter, Rowlf, Fozzie and the gang became much more readily available. I think the writers are having some fun bringing them back.
Still, more Gonzo is always a good thing.