I always thought nav' beacons should be more important, somehow.
Maybe they could become a focus for some kind of PP activity, whereby different factions within a system continually try to "capture" the nav' beacon and doing so might prevent that faction's enemies jumping into the system?
Democratic factions would leave the nav' beacon open for all to use, nationalist factions would exclude their enemies, reclusive factions would exclude everybody and lawless factions would do, erm, something else.
It'd be up to players to gain rep' with a faction (if required) to gain entry into the system, either to pass through it or to try and shift control to a different faction for some reason.
Just a random thought for the day......