The more I think about MFS, the more I think that any original songs would have been clumsy and awkward in the final exact project. Original songs could work with some high tweaking to the script, however. But the funk soundtrack is an experiment that failed, that's what we all can agree on.
But MFS is the one I'd want to change the most. Not because it's a bad film, so much as the film had so much potential and wasted the crap out of it. And I blame the hack Nickelodeon show director who was using the movie for street cred (and look at the "gems" he came up with... the second Garfield movie... Hop... really?!) Now, this is just a guess, but the reason Brian Henson probably couldn't direct that one was because of the "Eastwood rule" where you can't fire a director and replace him with any of the actors or producers of the movie (and you thought the empty chair rant was bad). They fired their first director and stupidly hired Tim Hill. Well, I'd replace him with someone who was competent and knew how the Muppets worked. Frank Oz clearly would have been off limits too, just so you know.
Other than that, I'd keep the entire house full of Muppets through the whole movie, remove the mundane activities that were so freaking important to Tim to have in the movie, have Kermit be a little more concerned about Gonzo and a lot more excited for Piggy's television gig (his lackadaisical appearance in the movie is totally unacceptable, as Gonzo's going through some deep stuff), keep all the sci-fi movie shout outs and Uncle Matt in the script Joey put in there, and above all, the big escape scene needed a HUGE rewrite...well, except for the "Doctor?" "Doctor!" "Two Doctors in a hallway" bit. That was hilarious.
As for the obvious not listed movie, know how I'd improve MWO? Rip up the freaking script and go with Kermit: Prince of Denmark. If any resentment I have for MWO shows up in anything, it's mainly because an awesome movie died so a mediocre and obvious mash up grew out of it.