Any comments I could make about MT must be taken with a grain of salt, because I missed the second season (it wasn't shown on Canadian TV and I didn't have cable at the time) and I've only recently started digging up some of it on YouTube.
That being said, my feelings about MT are summed up by a 2001 interview with Carroll Spinney in which he recalls a disastrous puppet performance that he delivered in the '60s and adds that Jim Henson came backstage afterwards and said, "I liked what you were TRYING to do."
And they really tried. There are days that I truly feel bad for everyone involved in MT - particularly the writers and the Muppeteers (of every vintage) and especially Brian Henson, who had the impossible task of both fiercely protecting and yet simultaneously enhancing his father's legacy only six years after Jim's death.
Occasionally, they nailed it. I got a grand charge out of some of the newer characters, especially Johnny Fiama and Sal (at their best in the Tony Bennett and Martin Short episodes IMHO), Bobo, and Pepe (believe it or not, I actually miss Seymour sometimes). Bits that should arguably have died in the script room - "Great Moments in Elvis History" and "Thor, God of Thunder" - turned out to be laugh riots. Even Andy and Randy, one-note characters whose jobs were to be thick and annoying, had their moments. (I wish I didn't giggle hysterically when one of them called Sandra Bullock "Miss Buttocks." I honestly thought I was more sophisticated than that.)
Whether they involved newer characters or beloved classic favourite, some of the MT moments are firmly lodged among my all-time favourite Muppet bits (yes, ranking ahead of much of the Jim-era content). Jason Alexander freaking out at the cast during the Hercules Poirot spoof; Whoopi Goldberg losing it when the rats sing Bob Marley's "No Woman, No Cry" too fast; William Shatner on the plane with Piggy; Sandra Bullock and Kermit updating "Mahna Mahna"; Michelle Pfieffer on "The Muppet Dating Game"; Cindy Crawford on "The Kermit The Frog Club"; Gilbert Gottfried winning a date with Kermit; Mickey Dolenz interrupting Bobo's retro '60s flashback ("I'm A Believer") to avoid paying his retro '60s alimony (I STILL can't believe that line!!!); Kermit's "Once In A Lifetime" and "Dancing In The Dark"; and, seriously, the entire Martin Short episode (climaxing with his finale with Statler and Waldorf).
I'm not blind to MT's problems, though. The first wave of Muppet recasts hasn't yet occured, so we had to settle for Animal being the only Electric Mayhem holdover (and minimal doses of Fozzie and Piggy) and a feeling that a lot of our old friends were missing all the fun. The show had such a frenetic pace and was more of a flat-out comedy than TMS, so we missed a lot of the softer, tender moments with the characters - no Ben Vereen singing "Pure Imagination" or Rowlf singing "What A Wonderful World" to a real puppy here. That had more to do with the overall tone of pop culture in the mid-to-late-'90s - the variety show format was pretty much toast and we were collectively more interested in laughing at ourselves (and each other) than stopping for a poignant moment.
I wish I could say I liked Clifford. I didn't. He seemed forced. I had a little trouble with Kermit's background role. And, as has been mentioned previously, a lot of MT's direct pop-culture spoofs had too many appearances (Bay of PigsWatch, Deep Dish Nine, Seinfeld Babies) or shouldn't have even made the show.
But I'm still glad they tried, and I look forward to having the time to see the entire run of MT someday. And I think anybody attempting to bring the Muppets back to a regular TV slot should look carefully at MT, not simply to avoid making the same mistakes but to remind themselves how well the Muppets work when the writing, the chemistry and the intangibles all blend together. This happened on MT far more often than we realize.