The faction system could be similar to the upcoming crew system, so there could be some correlation. Every faction would have its leaders/generals/dons. To be accepted in every faction, you need to apply and afterward, you're going through a testing system (skill test + knowledge about the rules). I am not really going to be very specific about this suggestion since it can become a litany, so feel free to share your opinion on this. Every faction would have a limited amount of players (15-25 members at max).
Possible factions:
San Andreas Newspaper - this faction would be only on forums.
San Andreas Army (already scripted)
Mafia (maybe they could own a black market with drugs, illegal weapons?).
At first, factions would be led by staff members for a short period of time, then regular players would take over.
I think this could be refreshing