Here's some example of weird colonization oversights in my current playthrough:
Seems like they eventually did recolonize some of them, but there's still a lot of decivilized worlds from frequent invasions that weren't ever reclaimed. Maybe they're too marginal even if they're habitable? Not sure. I did scoop up a couple of the ones that were decivlized (like Diable Avionic's Silvie, a class V)
Also, is it possible to get some tweaks to the reputation system to make it a bit less... silly at times? Transponders are a pretty big one, even factions who are Welcoming, Friendly, and even Cooperative still get pissy about transponders even if you're "well known across the faction" and are willing to go to war over it. No diplomatic immunity if you're an established faction, no ignoring the violation if you're friendly to them, no bribing them to look the other way, and they'll still bother you even if you're clearly an invasion fleet looking to gobble up any flounders that wander near you on your way to invade their world while running dark (Really, pickets should maintain contact on much larger fleets if their transponders are off rather than suicide diving to ask them about their license plates).
Similar case with Colony creation, if a faction is "Cooperative" and you're benefiting from trade concessions, that ought to cover establishing a colony in their systems and probably shouldn't ever do expeditions on your faction. It's kinda like if Britian sent in a team to sabotage or capture the industries of a france principality, it just doesn't make sense to do so given the political climate. Or if Germany attacked a US military base inside of their borders, just doesn't make a lot of sense.
Maybe worth looking at Saturation Bombings too, the AI factions don't seem to care reputation wise if it happens between two AIs, but if the player does it you get into a hot war with everyone. Realistically, it should have a more gradual curve. Allies of the faction that got bombed should get a pretty sizable loss in reputation (let's say 30-40) with you, neutrals to the faction that got bombed lose maybe like 20 reputation with you, and enemies lose maybe 10 reputation with you if any at all. It should also apply to AI factions as it's kinda weird that factions will saturation bomb each other and that seems to matter less to the political climate of the system than a jilted wedding arrangement.