Well, for one thing, we're probably so used to the older puppets, since new material (up till the movie at least) was few and far between, and our only exposure of Muppets was in the form of watching old tapes or DVDs of the movies, TMS, or other Muppety goodness. New puppets always take time to get used to, like a new haircut or something.
Another factor could be the fact that the Muppets aren't even built by the Creature Shop anymore, they're the work of a company called Puppet Heap.
Beau and I have to admit, we do find the newer puppets do look just a little too perfect... too clean, too symmetrical, too rounded... they haven't really had time to age a little yet.