"The Muppets Take Manhattan" is different in a lot of ways to every other Muppet Movie made so far. For one, it remains the only Muppet film not owned by Disney. As of 2008, the film still belongs to 20th Century Fox (CBS Fox at the time of its release) even though Disney owns the rights to the Muppets. Also, this film has a story line that's very non-linear, and events that are otherwise unpredictable.
Of course, it's very hard to beat the original "Muppet Movie" from 1979, especially since that movie had more memorable songs than "Manhattan" does. However, one way in which "The Muppets Take Manhattan" is better than "The Muppet Movie" is perhaps the surprisingly realistic scenarios. In the first movie, all the Muppets really have to do is go to Hollywood, walk into an agent's office, and they are immediately given a "Rich & Famous" contract. In this movie, the Muppets learn that they actually have to work for their desired success, and it's a lot harder to do that, especially in the entertainment business, than they initially thought. That's an important and often times overlooked message, provided one is willing to suspend the disbelief that the Muppets, being small and made of cloth, don't necessarily have to live in a spacious place or even eat respectively. Above all, their struggle to make it after graduating college creates a very good story. Another note: The celebrity cameos in the movie were cool, and they surprisingly managed not to take away the spotlight from the Muppets. That ability right there is a testament to Henson, and how appealing the Muppet characters were even to adults.
Where "Manhattan" falls flat, and this is where I'm sure people will disagree with me, is with some of the key songs, especially in the end. I thought the wedding song "He'll Make Me Happy" was too somber for such a happy occasion as a wedding. It sounded more like a song that's played at a funeral. Every time I watch this movie, hearing that song makes me unusually depressed, especially when the film begins on such an upbeat number as "Together Again" and ends happily for that matter. "Saying Goodbye" was a sad number too, but it fit better into the movie because the Muppets were disbanding and weren't sure they were going to see each other again. That last song was such a let down, and perhaps even added to younger viewers' misery of seeing their favorite Muppets leave the big screen.
"The Muppets Take Manhattan" is overall a good film, and one that marches to the beat of a different drum than the other Muppet films, including the newer ones made after the deaths of Jim Henson and Richard Hunt. Fortunately, the film marches in the same direction as well. I just wished the film ended on a better song that wasn't quite so melancholy. Plus, Disney should have gotten its hands on this film's copyright and given it a proper DVD release. Maybe it will someday. We'll see.