No offense to at all to them, but when a script is made better it isn't always the case that the veterans were the ones to do it. Star Trek II was hugely successful, yet written and directed by a completely newbie who'd never watched Star Trek a day in his life.
In this case the vets are in charge of Disney quality control. That's the main thing. Notes about Kermit being in the mansion and that the Muppets rarely ever refer to themselves as puppets (and when they do, it's a sly little aside done cleverly). Plus, I'm sure the Muppeteers made darn well sure the characters were as close to the characters we know and love.
However, it was that very same outsider angle that brought passion and vision to the film. Left to their own devices, as great as Jim and Kirk are doing they would have made some weird gimmicky movie we just couldn't get excited about at all. Maybe even another (gasp) classic retelling. And with C-List at the moment stars that fit poorly. I wouldn't be surprised if Schnooky or whatever that trilobite's name is would have a pointless cameo.
The Muppets showed such a brilliant blend of insider and outsider cooperation.
The Star Trek movies... I can't really comment on. I've heard even fans hated them, except a couple... the same ones that are absolute purists that forced themselves to hate the 2009 J.J. Abrahms movie that everyone else in the world loved. I actually JUST started watching Star Trek's original series care of MeTV, and I can see what the problem might have been. There's such an amazing style the show has, and it broke some barriers that never needed to be broken again. It left all too soon leaving animated adaptions, movies, novels, new generations and all that... they probably just didn't have the same feel no matter how hard they tried. And that's probably the problem. They tried too hard. Outsiders sometimes have better vision because the vets think inside the box too much.