silverfoe
First of all - the resources. Though now it's not really a reason to expand, the future universe update seemed to be centered around scarcity and forced interaction between factions that have access to that specific resource.
I like reversed faction point mechanic, with FPs generated by the hubs and requiring connection to the homebase, whether through claimed neighboring systems or warpgates leading to claimed systems, all the way to the HB, to "send" those points to be used somewhere.
So by severing this connection you would cut off the homebase and the faction from those points, possibly purchased effects too.
Right now FPs don't seem to do anything, so I'd have them being used to "purchase" some faction bonus, like even more mining bonuses for systems with rare resources. Whether for a single system or the entire faction space, one-time purchase or an automatic FP spending. The new effect system would be perfect for such mechanic.
Should NPCrew make an appearance, I wouldn't oppose also being able to spend the faction points to hire bunch of crew members for assignment to various ships and stations.