What they need to be is re-imagined. Make them a significant PvE gameplay element. Make them scary, with all kinds of top secret equipment (cloak disruptors, armor upgrades, unlimited cruise disruptors, CODENAME weapons... you name it). And increase their spawn rates significantly. Basically Discovery boss fights.
Then populate the guard systems with stations / wrecks / depots containing all kinds of contraband and quasi-legal stuff (the unused mission cargo from vanilla as commodities might be a good start), and maybe some RP based commodities such as Battleship / Battlecruiser / Prototype blueprints. Maybe some Sci-data too as an alternative for obtaining Sci-data for people who don't want to hunt for anomalies.
Then you have a nice, challenging PvE environment that can be used to RP common tropes (stealing military secrets or secret technology... or kidnapping important military personnel). Basically something that needs to be done as a build-up before you pull-up a totally bull____ story how your tiny faction managed to obtain access to highly classified technology / ships. It could be used as an alternative when there are no / very low numbers of player run Navy factions you could RP with. But it needs to be a hard alternative, requiring either specialized ships (high level cloak) and lots of luck or a major group effort.
Think the Proteus Tome mission in Tekagi's Arch but in multiplayer, with your faction's story at stake.
