The main reason why The Muppets was made was because Jason, and the other writers, were sick of the gimmicky movies hat were being made (and I guess ones he heard about that weren't). If the movie succeeded in one thing, it was showing that the Muppets can be in a movie where they play themselves without some crazy theme that's completely inorganic to the film.
Time Travel and In Space are the very same kinds of Muppet movies that Jason and the rest would have dreaded... and in a sense, we probably wouldn't be too happy with them either. Not that Kirk's "in Space" movie wouldn't have been more enjoyable than MFS ever was... but deep down, we know Jason and Stoller were right in doing the right movie at the right time. Something like In Space or Time Travel wouldn't have lit the fire under the collective bellies of Muppet Fans, especially the ones that forgot how much they loved the characters due to the meh-ness of the last films. It wouldn't have relaunched the franchise, and I don't think they could sustain it just yet.
They're not quite in the stage of playing with house money just quite yet. The first movie had to be a hit to get a second one, the second needs that same passion to become a hit to make a third movie. They can do whatever the heck they want then, but right now, we need something as passionately driven as the last film.