Ok, sorry, but I don't think there's really any comparison here.
I like both "A Muppet Family Christmas" and "It's A Very Merry Muppet Christmas Movie". But "Muppet Family Christmas" has to be my favorite. It's one of the very few times you see characters from The Muppet Show, Sesame Street, and Fraggle Rock all interacting. (They even sort of worked Muppet Babies in there too- with the film of The Muppets' first Christmas together!
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This special is definitely some of Jerry Juhl's best work. I liked Kermit and Robin's interchange with the Fraggles in the cave and it was also cool that they came and joined the Muppets later on during the Carol Sing. (Even Uncle Travelling Matt shows up!)
And I love a good running gag- like the "Be careful of the icy patch" bit. And it may be one of the strangest pairings I've ever seen, but it was really cool seeing Big Bird and the Swedish Chef singing "The Christmas Song"- that was one of the best parts. (I think I was crying with the Chef at the end!
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The special took advantage of so many great chances for interaction. Like Bert and Ernie telling Doc that "bunkbeds" are "B words" and telling him that where they come from, that's small talk. LOL!
And Janice and Cookie Monster's interchange. "Look what I've got. Christmas cookies!" - COOKIE!!!!! "Who was that strange blue creature?" Animal- "That my kinda fella!" LOL!
Great exchanges like that made this an awesome special. And of course, there's tons of great Christmas music. I think I like almost any song when the Muppets are singing it and that's especially true of Christmas music. "We Need a Little Christmas Now" is a great song!
And Jim Henson's cameo at the end made the whole thing all the more special!
However, there are good things to be said of "It's A Very Merry Muppet Christmas Movie". For one thing, it's nice to see the continual integration of classic TMS characters with Muppets Tonight characters. It's unfortunate that Clifford doesn't show up, but at least you see his picture on the wall. It's always neat when little things like that are thrown in. And the movie managed to reference/parody almost every major Christmas movie!!! For a huge fan of Christmas movies like myself, that was awesome. The title itself is a reference to "It's A Wonderful Life", which of course is dealt with even more with Kermit getting to see what The Muppets would be like without him. (And I loved Yoda's cameo!) The snowman narrator is of course, a reference to Burl Ives' character in "Rudolph the Red-Nosed Reindeer" (I think I'm right on that anyway) And Rizzo's red nose obviously referenced Rudolph later on. The whole gift exchange thing at the start was a great parody of O. Henry's "The Gift of the Magi" (a beautiful story by the way)
(And Johnny Fiama's reaction was perfect! "Gee, thanks Sal." And Bunsen and Beaker were hilarious in that scene too)
And Fozzie did a funny parody of "How the Grinch Stole Christmas". And there was even a reference to Steve Irwin- the Crocodile Hunter! And one of my favorite scenes was the frog with his tongue stuck to a pole. (And the frogs telling him, "Come on. I triple frog dare you!") LOL!!! That was a reference to a classic 1983 movie- "A Christmas Story"- one of my favorite Christmas movies.
And there was still a cohesive story running through that was really good. And I know Scooter's voice was a litte off, but it was great just to have him in there. And to see the Muppet Theater after 21 years! And Sam had some good lines (and a very interesting alternate life!)
But I think one of the best parts was Kermit and Gonzo's song "Everyone Matters". Such a true message! And that was really great. And I also liked that Gonzo got to have a fairly large role in the movie, along with Fozzie. I don't think it will ever be the same as "A Muppet Family Christmas" or "The Muppet Christmas Carol", but it's a pretty good Muppet Christmas addition all the same.