Kermit was in that weird phase where he wasn't being used much. I don't see why there wasn't more Gonzo, but he had his fair share of screen time.Actually, I always felt the few frequently used classic Muppets (Kermit, Gonzo, etc.) took a considerable backseat to the new characters.
Oddly enough, I do consider most of the new characters the show's greatest assets. To the point where some of the older characters used weren't really given sketches that worked with them. Deep Dish Nine, for example. They got Piggy, but they didn't get what made Pigs in Space special. ERERO was cute, but lacking, with Fozzie in Dr. Bob/Rowlf's role. However, things like Johnny and Sal, Pepe and Seymour, Tales from the Vet, and the UK skits as well as one off pop culture parodies more than made up for the lack of classic characters. The good newer characters pretty much carried the show for me.
Of course, if MT was made today, there would be a definite lack of new characters as most of the beloved classic characters have been recast. Rowlf, Scooter, the Electric Mayhem... if there was a new Muppet show, we'd see a lot more of them while Sal and VanNeuter need to be recast (unless Brian decided to freelance to Disney, but he's too busy currently with Henson stuff), and the rest of them we hardly saw anymore anyway.
Now I needn't feel to repeat myself, but my favorite format, hands down, was Jim Henson Hour's Muppet Central segment. If they were able to merge the best of The Muppet Show, JHH, and MT, that would be the direction I'd like to see another hypothetical show.