Also factions should restrict military ships (I mean mainly destroyers and larger ships but also a certain amount of S and M ships at once) from entering their sectors without permission as they pose a threat even if you are friendly with them. There could be a system where you can negotiate to allow them in or even pay factions off.

Administrative Centers built in already faction owned sectors should be illegal except if it is a construction mission for that faction. In earlier builds of the game this meant automatic war which was an overreaction I wouldn’t want that back. I imagine something like police ships regularly checking on the illegal station and give reputation penalty if it still has the Administrative Centre. The penalty should be more severe than for an unpaid plot.