I don't know. Some goodies here and there, like a flagship or special ships for SOF operators would be nice. A separate shipline for faction members however doesn't strike me as a really good idea. All it'd do would be placing an unnecessarily high workload on the devs with little to no reward. In fact, I think it would be a really, really good idea to cut down on the amount of available ships - many factions that by no means have access to the necessary infrastructure and brainpower to design and build their own shipline do not only have their own fighters and bombers, but, in some instances, warships, too. Big kudos to the Xenos here. I'd love to see more factions following their example, placing RP over getting shiny new toys, but I guess I better keep dreaming...
To get back to the topic: No, I think it'd be much better if you'd simply allow factions to police their own ships. Some factions would greatly benefit from being made adminrep-only, too, but that's a different story altogether.