The only problem I have with The Muppets is that there was too much concept in the run time they were allotted. They cut out quite a bit, but the movie had a break neck pace that made the most of every single moment. Other than the Me party segment, nothing dragged the movie down.
MFS is quite the opposite. There are just too many drags in the script that stop the movie cold and ruin the pacing. A lot of it was Clifford checking mail, Kermit painting the house... and just droning portions of too few Muppets acting bored. The card playing scene? What was that about? Gonzo rushes in and says "I'm from OUTER SPACE!!" He could have just yelled that off the roof tops and got the same reaction of characters running out to see what the explosion was. Not 4 of the Muppets bored to death playing cards.
Here's how the COVNET break out should have gone.
Kermit, Fozzie, and Pepe should have been the only ones that broke in, with Floyd and Animal in the car for back up (having left Bunsen and Beaker behind... I still think that part was pretty brilliant). Piggy was back at Cape Doom covering the story, cutting to a sequence where she worries if Kermie is safe. Using the invisible spray, the three of them split up undetected looking for Gonzo (who just walked out of his holding cel after talking to the sandwich... Bobo forgot to lock the cel behind him), and the invisible spray wears off at compromising moments. They aren't caught, and manage to remain incognito. They all regroup to think up another plan to get Gonzo. Fozzie asks "okay, now how are we supposed to rescue him?" Gonzo pops up behind him and says "Find Who?" Fozzie replies "Well, Gonzo, we have to go find Gonzo." Realizing that, Gonzo points out they still need to find Rizzo. Fozzie asks, "Yeah! Where is he?" Rizzo pops up and says "WHere is who?" Fozzie replies "You know Rizzo, we have to... WOULD EVERYONE CUT THAT OUT!?!" Just a corridor away from escape, they manage to sneak closer to the exit without making a scene, even though it's clear that Gonzo escaped at that point and they just started to alert the guards. Meanwhile, back in the van, Animal grows impatient, Floyd is unable to hold him back. Animal storms the base (the guard is still affected by the Mind Mist), causes a ruckus before the others are almost out, causing a massive chase that leads them in circles (where they run into, and knock over Van Neuter, who himself is being chased by the rest of the rats)... there's large spread confusion, they use the door in a jar (to the same extent in the film) and manage to escape. Gonzo points out that it's almost time for the aliens to land, and they speed off in the Mayhem Van with Agent Singer and Bobo in hot pursuit.
Meanwhile at the landing site, everyone gets sick of waiting for both the aliens and Gonzo (both are late), and everyone else seems dejected until the Alien Gonzos touch down. After asking where the one called Gonzo is, one of the Muppets waiting says that he didn't show up yet. The head alien says "We're a very busy people. Maybe we should try again next century." With that, the Mayhem bus careens to the beach, passers by jump out of the way. The bus skid to a stop, Gonzo jumps out of the door, runs, collapsing at the base of the ship and says "I'M HERE! I'M HERE!"
And basically everything's basically the same from there.