Factions, factionettes, indies... That's a flawed concept altogether. There should be just factions, but not in today's sense - you set them up and can never be sure whether your official status and rights is worth the trouble you're having with those nominally under your authority.
Instead Factions shouldn't be set up, they should just exist as a game element and for the sake of governing every aspect of the faction as if it was the mystical NPC guildmaster, queen, president and whatnot. Except instead of this mystical line of text pretending to be the leader - it should be people. Chosen by the people, for the people and er... Against the people! (Or something like that)