Let's see... Uh... the Muppets were no more "just there" than MCC. I mean, really, you could have done the whole thing without the Muppets and just the creature shop and it would have worked just as well... Kermit was fatally lobotomized in MFS (I know it was Gonzo's movie, but you'd think Kermit would have been a little more supportive instead of heck bent on painting the house).
And Muppet Wizard of Oz exists and is a thing.
Seriously. Muppet Wizard of Oz is a thing and people chose to complain about The Muppets.

And if it wasn't for the "novice fan fiction writers," the long time staff would have came up with something even worse than Muppet Wizard of Oz. At least a fresh perspective didn't leave us with another Pop Culture Joke laden movie where half the jokes are already dated that comes off cynical and blindly groping around for target audiences and in the end, losing the core fans.
To be fair, MFS was saved by the newer characters... not even Johnny Fiama could save Muppet Wizard of Oz. It's like the criticism I hear about Man of Steel. Oh, so you'd rather watch Superman 3? Like one of the worst films ever made? The Muppets was all about brand reintroduction. The second film can only be better and more Muppety.