It's nice to read some discussion of the film from folks who know more about Muppets history and context. I had an extremely negative reaction to the new film and was, frankly (pun intended), relieved to find that Frank Oz and, apparently, some of the other folks from Henson studios, had criticisms of the script.
For me, the script felt like a shallow recreation of someone who had tremendous affection for, but not deep understanding of, the characters in the Muppets. The screen time devoted to the human characters was probably the worst part, as it was not sufficient (nor was the script resourceful enough) to make it anything more than an incredibly superficial cliché, but it was enough screen time to reduce the breadth of story allotted to the Muppets themselves considerably.
But for me, the saddest thing was just how few decent jokes there were. Great jokes are hard to write, obviously, and the Muppet show (like almost any show) has plenty of misses, too. The other Muppets films have ups and downs (Muppets Christmas Carol is a masterpiece, the product of skill, luck, and divine inspiration, while Treasure Island is a more mixed bag), but I've never seen an entire film so filled with wet sacks of dead-on-arrival attempts at humor. Most of the movie's meta jokes function mostly as preventative apologies for the script's half-assedness.
Whether Oz saw the final script or not, I'd be surprised if his lack of enthusiasm wasn't related to the utter lack of vitality of the characters themselves, something that - in my opinion - was certainly not resolved in the final script.