I am a bit bias, I don’t like/do raid missions, just dashing and using stealth, reaching specific tiles in a few turns, and suddenly all frozen, you win, it is a bit silly
But I envision aggressions as act of war, two warnings is too much,
one warning and massive lost of reputation -20 is my suggestion,
and if you attack an ally to raid/sabottage/steal aircrafts that means war.
About diplomacy, I have REP 100 with all factions easily because destroying lairs(+10) and citadels(+15) provides too much REP points, well, I could avoid diplomatic missions, stopping it, I will try next time. But it would be ideal if you have to choose only one faction for alliance, blocking the others.
Attitude in havens right now is irrelevant, they don’t have own mind, if they are pissed off, very, they should attack PX bases, or if they are very grateful due to repairs, PX choices in POIs or multiple haven defence they should offer armor/weapons, and very advantageous trades
I don’t understand why you have to lose REP with other factions(hostile or at war) if you defend another faction, and factions total war in March is a pain, but I suppose is the way to accelerate HPC going down and putting pressure in PX.
And new Ancient sites should be tradable, factions need power to fight Pandorans (and other factions) so you can trade those under PX control, you get resources and they get new tech, making them stronger.