I get what you're saying... the way the movie turned out, it might as well have been a Creature Shop film, with JHC Creatures just as the ghosts. But I really like the concept of having the Ghost of Christmas Past being a puppet filmed underwater. That's the part of puppetry that engages me the most. Experimental effects like that. Jim would have been proud for that alone.
But when it comes to the actual project, there is one huge problem. It's too darn accurate to the book! It's even more accurate than straight up adaptions. MTI was a much more fun film because of how much stuff that had to be made up just to accommodate other characters. MCC had no such flexibility. The only major change was giving Jacob Marley a brother to accommodate both Hecklers and clumsily adding in that Fezziwig's was a Rubber Chicken factory, yet not elaborating on that.
Though I will say, since most of the characters were yet to be recast, I don't really see how many Muppets could have been used. Bunsen and Beaker could have been funny as Ghosts and using some weird malfunctioning scientific means to go back in time. Too bad they went for accuracy instead of funny.