The concept of "seasons" is dying off. It was mostly an American phenomena where networks were willing to pay for runs of 40 episodes of television shows. This gradually dwindled to 24 episodes as they figured out viewership dropped off in the spring and summer months, and their biggest sponsors paid for the bulk of advertising between September and January. Elsewhere in the world runs of episodes were called "series", and you would get anywhere between 13 to 3 episodes each new series. In America a "series" was every episode of a show, since the season including reruns lasted the entire year and ran right into the next season, giving the effect of the same show being on continuously. But if you watched programs in the UK, a run of episodes would be much shorter, and the next run of episodes would not be called the next season, but considered an entirely new series. And new series were filmed whenever. They weren't broadcast on a season schedule. The first 13 episodes of something like Monty Python was followed by five months before the next 13 episodes, and then two years before the next 13 episodes.
Viewership in America is changing. Shows are now being sold on a worldwide basis. All of this is contributing to the new normal being seasons that are shorter than Americans are use to, and airing inconsistently. It is beginning to make more sense for both the networks and producers. For the networks, shorter seasons means committing less money when the risk of committing money to the standard 24 episodes would force a play or pay situation where a season would continue to run even though the ratings have dropped. For the producer, it is easier to retain the original cast if they only have to commit to 6-13 episodes rather than the previous 6 months they were stuck filming a season, which often meant they either had to pass on movie roles, or quit the show for a movie role and have their character written out of the series. And filming less episodes means a season no longer needs to be padded out to a full 24 episodes with weaker episodes.
If MST3K is going to do a 6 episode season, it is possible that we may eventually see two or more seasons in a year, depending on cast availability and how often Netflix is wiling to finance the next season. It also makes more sense for Shout! Factory. It is much less expensive to sell a six season box set ( they still need to pay royalties for each individual movie ) which can be sold for a much more reasonable price than $90, something more like $40 fir a season set. Also, concentrating on fewer episodes per season allows Shout! Factory to negotiate for higher profile and more recent films. The original MST3K relied on public domain and cheap independent films. But if you ever want to see something like Batman & Robin on MST3K, then it could only happen if Shout! Factory is negotiating for and budgeting for fewer episodes.
Another bonus for Shout! Factory would be less lag time between the Netflix release and Shout! Factory release. Netflix wants a longer exclusive to insure that every episode is rented, rather than having viewers who only got around to renting half the episodes and watched the rest on DVD or Blu-ray. Figure a six month season would be about half the lag time between Netflix and Shout! Factory release. So everyone is happy.... well, except the viewer who wanted the standard 24 season.