At first, Sci-Fi was VERY concerned with making the show sci-fi-oriented, and that's part of the reason why they didn't buy the rights from the earlier seasons. Other reasons include the fact that the first few seasons were VERY spotty in terms of joke density and good delivery and the fact that other parties were gradually acquiring the rights to the films, making it impossible for the episodes to be rebroadcast.
Sci-Fi Channel's misdirected concerns about MST3K also forced the show to create a linear (and VERY stupid) storyline involving travelling through space and time in some kind of epic adventure. Needless to say, fans hated it and Sci-Fi eventually gave in, letting the show's creators do what they want. This is why the later Sci-Fi seasons are not all sci-fi and the interstitial sequences stopped including some lame plotline and went back to random skits and gags. Now, however Sci-Fi is gradually losing rights to the movies in their own episodes (like Diabolik, for instance), and that's why they're showing fewer and fewer different ones in reruns. They'll be doing reruns for at least one more season, but they mostly show the last season or two now because of the licensing problems (and to avoid reminding people of the terrible Planet of the Apes plotline - ugh!)
If anyone is interested in the early episodes, my brother and I have a fairly good collection (about half of all the episodes) on tape, including the 3rd Comedy Central season in its entirety and most of the last 2 Sci-Fi seasons.