Gonzo was very different in MFS. There were hints that he did crazy stuff, but he was depressed for most of the movie.
The older stuff is better because the older stuff was done using 3 of the greatest Muppet performers of al time. Richard Hunt, Frank Oz, and of course Jim Henson added so much to the shows and movies and that something has been missing. It's not just the characters; it's the smooth performance and delivery.
It seems that MT was a series of bad jokes and puns with no real substance. There was no rhythm to the shows. Many guest stars hammed it up. The Muppet characters on MT were more like parodies of the Muppets. Brian Henson did a lot of over acting and Steve Whitemire (I'm sure it's spelled wrong) did a lot of bad jokes that were bad bad and not funny bad.
The Muppets were great in the past because they were serious in what they did. It was funny, but not "Hey look! We're being funny!” It was a dryer wit and professional delivery. This carried over into MCC and even MTI, but then MT and MFS were too "zany". AVMMC got back on track.
The new characters work well in places. Sal works with Johnny, but not as a main character. Pepe works, but Seymour doesn't. Phil works in small doses, but not in 10 minute bits. Clifford works with the sun glasses and cool attitude, but not with the bug eyes and awful talk show host personality. It's a matter of balance between new and old characters. The new characters have a place, but they should replace characters like Fozzie who almost never showed p in MT.