I like the idea being part of a county (city state/npc faction) and stick to (defend) the area you belongs to and exert the influence of your country outwards into the wild wasteland. I think it would give a clear meaning to play for every player/faction besides mindless PK or TC (after lvl 21) and also gives a little bit tastes of RPing.
I think player faction as a whole should be join-able to one of the countries or towns, maybe linking some of faction names with the countries/towns it belongs to is a good idea.
Except law abiding and self righteous NCR, greedy hub and BY, communist SF and hypocritical VC as powerful countries there should be less powerful towns to join. You or your faction as a whole could be trappers, slavers, miners, mafia or radiers to fight for survival and limited resources. Maybe in the future the majority pk factionse will choose a faction name belongs to raiders or mafia because mindless kill of players (citizens) will be punished (put into jail or something) if your faction belongs to one of the lawful countries. Those who likes PK can do PK and those who dont will not forced to be PKed.