The way Pandoran structures are currently generated is definitely problematic, because
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it doesn’t fit the lore (2 Nests within each other operating range form Lair, while the Nests become abandonded, and same with 2 Lairs and Citadel),
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Pandoran colonies that don’t have any havens to attack don’t do anything besides contributing to a hidden max cap, and
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The whole thing is really governed by hidden counters telling when to spawn a new base or to launch an attack.
All this adds up to an unsatisfying feeling that the whole thing is just arbitrary.
And there is also this:
The @noStas and @MadSkunky idea is pretty good, imo