Playing hidden base whack-a-mole isn't fun and it becomes chore busywork that distracts the player from what they're supposed to be doing.
I feel this. With Pathers, I know I have a ticking time bomb where I can spend a few months either exploring the other side of the sector or raiding core worlds for missing blueprints (or hunting deserters) before I need to stop what I want to do, use Intel exploit to find base, and kill it before I can play in peace for another year. I try to get all active pather cells in all colonies synched to one single pather base so that I do not need to kill more than one base per year. In the meantime, I get invasion alerts from major factions, which I completely ignore (if my colonies are strong enough), and sudden pirate activity, which I cannot ignore and must drop what I am doing and deal with the problem (which may mean burning across the sector back home).
Having a colony threat alert every few months that only my fleet (of space cops) can fix means no time to do fun stuff unless I can completely ignore most or all of the threats. Like in Nexerelin, I almost feel like the janitor or hired hand that can be fired at any moment instead of the leader of my faction.
I would like it if I can round up Pather cells and exterminate them permanently. Without old Industry Planning 1 and nanoforges adding to pather activity, there will be no way to avoid pather cells if the goal is meeting demand and obtain self-sufficiency. Of course, killing pather cells with brute force probably will not happen, so the next best thing is to order fleets to kill bases for you.
And because other factions do not attack bases threatening them, player needs to kill some of the pirates to prevent them from decivilizing some core worlds and permanently reduce your income. (Decivilization is fine once the goal becomes kill all factions and conquer the sector, but not before then.) They have no problem sending multiple huge fleets to attack my colonies. Why don't they send those fleets at pirates and pathers that are actually harming their colonies, or at other major factions' whose colonies are smaller than mine?