1. Organize ingame events. Base the lore on these events. Allow only the official factions to attend to these events. This way, factions would have something to work for. Trading, mining and whatever events can be invented for commercial factions and battles for the fighting factions. All shown on updated influence or territorial maps.
2. Give POBs to official factions only. Allow them to build stations with no limitations. The equipment they produce can only be sold on RP basis, not on the open market and the faction decides who may get it. If they want all their indies to fly with their jump cloaks, it's their problem.
3. I'd suggest restricting caps but since that will never happen, how about restricting equipment? Restrict capital armor upgrades. Only official factions can mount them. I'm an indie, I want that ship. If I want a CAU, I'd have to enter a faction and work my way up the ranks. And this brings me to the following point...
4. Don't allow the same person to be the leader of a faction for more than a year. Each year, the factions would have to elect a new leader (ooRP or inRP, that's their business). That way, a simple indie could work one year to gain influence within an official faction so that he is allowed to participate and maybe become the new leader, so he can have his CAU 8 BS firing lazors!