Sorry if everyone already said this stuff but I don't got time to read 9 pages of forum posts:
1) Plan out your colonies so that you avoid Pather cells by keeping Pather interest below 7. Without using AI cores or having mismanagement penalty, you can have: 1 pristine nanoforge + refinery planet, 1 autonomous drill planet (ideally with EXTREME HEAT for cryo bonus), 1 soil nanite planet with light industry, 1 gas giant with vortex, and 1 fuel refinery planet with synchotron.
2) It makes a LOT of sense to colonize multiple colonies in the same system and have a Military HQ on at least one, ideally with cryoarithmatic engine on EXTREEEEME HEAAAT.
3) I THINK, but don't know for sure, that pathers and pirate threat don't trigger until Size 4.
4) You can get
Spoiler
Kanta's protection to completely eliminate pirate threat
. In my game I had three choices: 100k bribe (didn't work, reduced rep), burn relationship with highest ranking contact (what I chose and it did work), spend a story point to offer
an unspecified future favor.
5) The code for danger reduction for destroying hostile ships in-system is bugged. Apparently when pirates/pathers are non-hostile, they don't count. Will be fixed in the next patch.
6) There is a quest to completely eliminate Pather threat, but at the cost of
Spoiler
giving the Pathers a functional Planet Killer missile
. That quest is bugged, though, and there is no way to eliminate Pather threat ATM. Will also be fixed in the next patch.
I can't wait for that new patch/hotfix/warmfix. My game is almost unplayably annoying without being to finish that quest.