One thing it was missing was Muppets! The Pet Shop scene was the only place we really saw a lot of muppets. The rest of the movie lacked the.
Here is a list of places child versions of classic muppets would have fit in, without even needing lines:
1. When Kermit visits the farm and sees the pig. Piggy could have been shown, in a pen that Kermit runs past, sitting in a puddle of mud looking disgusted while in a pink dress with that bow in her hair. Easily could have been done, no lines needed.
2. Rowlf could have been in the pet shop in a window.
3. Rizzo could have been a rat meant for being fed to the snake in the pet shop, but escapes.
4. Fozzie could have been seen on the side of the rode watching that truck go by or something.
those are the only 4 I have right now, but there are plenty of places to add in Muppet Cameos who don't have to add to the story, thus messing with the time line, but just be there to add more muppetness to the movie.