So I had this idea floating around for some time which again surfaced during previous post. What about assigning your Runts to devise mission plans that, once researched (akin to Prizes), would affect mission generation in current/following month? Ability would depend on some kind of mid-late game techs (Advanced Tactics, Art of War,... whatever) and having completed the mission type already (or multiple times).
For example: "Marsec Protocol" (I'm bad at names...) would increase that faction spawn rates in Geo. Either for current month, next month or next 30 days. Besides affecting Geo RNG it could be used to force a mission from already available pool of missions (Space Freighter, Mansion, Demon Shrines, Cannibal Camp, etc), or just spawn a desired enemy ship. The rarer/more complex the mission the more time it would take to manufacture/research. It could go in other direction - to reduce spawn chances of certain mission types. For example: filtering out radar frequencies for Megapol / Dark Ones detection for a month.
Whole idea is to reduce dependence on late-game RNG and give that power to player. It's not hard to foresee RNG becoming even less favorable as more missions get added, giving raise to situations of chasing one missing item that is bottle-necking everything or, more commonly, rare items you need more of.