I like Laura's present idea of giving Official factions slightly better IDs, but considering the fact you can emergently Rp your way into a better ID in the present state of the mod, shouldn't factions just make more requests?
Perks by default sounds fun as well, however, but I would have it in addition to the current system, instead of substituting. Anything to get people to join official factions is a good proposal.
Edit: Having been an Unofficial faction lead for three years in various factions, I don't differentiate between OFs and UFs. I treat them exactly the same. Now I'm doing a lot of Official Faction Roleplay, I act InRp as if the UFs have the same privileges I do. It works out rather neatly. Nevertheless, Official Factions should have more staying power since they have actual lore control. Let the OFs have bigger ZOIs and better gameplay than the UFs and Indies, because that's how you get people playing them.
THE SYNDIC LEAGUES
(A co-operative of Rheinland's Shipping Unions, retired from a life of piracy.)