As you're playing this mod, obviously, you encounter tons of missions, enemies and equipment and progress further by unlocking new stuff. Most of the gear has an "expiration date" past which you don't want to use it, because you have more powerful stuff already. Nobody will attack alien colony with a pump-action shotgun, for example.
Same goes for missions - you do cult apprehensions, but once you progress far enough you leave these to council salvagers, because you have more important tasks and eventually you terminate all cults and their remnants aren't something you bother yourself.
However, I noticed that's not always the case - in my last in-game month I've gotten tons of hybrid-related early missions despite already conquering their hq. It was farm after chemtrails after farm after chemtrails non-stop, even aliens gave up during this month and haven't sent a single ufo. I checked the wiki and these seem to have no trigger to stop them from spawning!
May I ask why is that? I have cyberarmor and lasers, in these missions it's a miracle if my soldiers get hurt at all, for all practical reasons I'm invulnerable and it's a duck hunt. These missions stopped being fun because of this, they became "obsolete" and I want them gone from my save.
"But you can skip them their penalty is minimal and you get tons of points from ufos and bases and stuff" you might say - true, but there are only so many missions per month and I'd rather get the ones I need to progress and are still fun to play rather than end up with the mission pool clogged by stuff I no longer need nor does it provide any challenge whatsover. If council salvagers can deal with cults or monsters past a certain point, why is hybrid farm assault suddenly a problem?
So, tl;dr: My suggestion is to include "disable spawn trigger" for every mission from a "completed" questline so the player has a higher chance to get what is currently needed. So many chemtrails and farms, yet it's been months since I researched cult of apocalypse communion and I'm yet to have a single mission spawn.