I do like MFS even though I harp on it a lot... but the one thing I think they did right was have an antagonist who wasn't a villain. Same thing with Follow that Bird. Miss Finch, the main antagonist wasn't evil, she was doing what she thought was right, same deal with Singer. These aren't bad people (or birds), just self righteous and don't realize how harmful their actions are. I'd love to see that explored once again.
Doc, Tex, Rachel Bitterman, and Nick Holiday were the standard black hats in those films... Tex is the only one of the bunch who has some sort of catharsis and changes (even if the final film suggests it's because of a large Flintstonian bonk on the head), but the others wind up getting exactly what they deserve in the end... Nothing for Doc and Bitterman, jail for Nick.
I don't list Scrooge or Long John Silver because they're pre-existing literary characters... though Long John would be a tied second favorite with Charles Grodin...
I do think that may have worked for a Muppet film... but to launch the film and grab people's attention they needed something that's a little more mainstream in tone. The Piggy/Kermit Paris scene suggests the film desperately wants to be slower paced and a little more adult. I'd say if there was a problem with the 4th wall gags, it's probably because they're trying too hard to be like the first film or maybe GMC, but those jokes aren't really there in their own movies (Forgetting Sarah Marshall, Knocked Up, etc)... but I don't find the pacing as utterly offensively sloppy as half the other kid's films out there. Those ARE ADD.
Still, it seems that's the way some of the other Modern Muppet projects turned out... though, if anything, MFS's pacing is too slow in the middle. Doesn't really bug me that much, and I bet it's all about the editing... next time if they cool it and tone it down a little, make it more MTM paced, we'll have a stronger film over all.