This might be better for its own thread (though I can't figure out a good thread title for the subject), but here goes...
Latley, on the Tough Pigs forum (and I think I've seen this brought up on the Muppet Central forums, and it is brought up as well in Jim Henson: The Biography), when people discuss Jim Henson's works from the 1980s, particularly The Dark Crystal, Labyrinth, The Jim Henson Hour, and shows that didn't make it past a pilot, people say that Jim Henson's later works focused a bit too much on newer technology while actual story and character development was typically weak. But when it comes to story, it seems like Jim Henson didn't write much of his work in the late-1980s, or at least wasn't credited as a writer. I think The Dark Crystal is the only movie he did where he got a writing credit (though I think Jim Henson: The Works says that he worked on the first draft of The Muppet Movie script, and Jim Henson: The Biography says something about him working on a draft of the Labyrinth script). So it might be the problem of different writers, as far as story is concerned.
Of course, the majority of Jim Henson's biggest successes didn't have much plot focus. There's Sam and Friends, the various commercials, and guest appearances, which lasted just a few minutes long. The Muppet Show was a variety show, with songs and sketches taking priority over the backstage plots. Many of the Muppet specials Jim Henson worked on didn't have much plot. Some were variety specials with no real backstage plot, some were musical specials with barely a plot (the John Denver specials can just be described as "John Denver and the Muppets do a Christmas variety special" or "John Denver and the Muppets go camping at the Rocky Montains and sing songs"), the 30th anniversary special didn't have a plot... Jim's last two Muppet specials, A Muppet Family Christmas and The Muppets at Walt Disney World, were closer to having actual plots, but at the same time they also had several subplots, running gags, unrelated songs, and other random stuff that had nothing to do with the plot. But aside from the movies it seems it wasn't their strong suit in giving the Muppets their own narratives.
Of course, Jim Henson did do a lot of things that had more plot focus, including the Tales from Muppetland specials, Emmet Otter's Jug-Band Christmas, The Christmas Toy, and Tale of the Bunny Picnic, but off-hand I'm not sure if he wrote any of those (I know he directed most of them). And of course Fraggle Rock was the first Henson series to focus on plots as opposed to being a variety/sketch comedy show, but Henson had little involvement on those and didn't write any scripts for that series.
Of course I think Jim Henson came up with the ideas for the majority of productions he did, and probably sent notes on the show concepts to writers and such, even if he didn't write the scripts.