I think entire cities would be too much. Maybe quadrants of cities (i.e Freeside) would be held by gangs (guilds, clans, etc) but not the entire thing. If these areas were to exist, they should be predestined areas that require domination of a key point (i.e. a fortified position).
As for entire guilds being organised in that manner, that would be curious but R&D should come from individual merit such as those who are more scientifically focused as opposed to fighters. They should then be able to craft within a post or store owned by the guild to sell these goods. So gunslingers bring in MATs, science buffs give it. As for research, there should be quests for blueprints in certain areas held in radiated vaults full of mutant things that are held on a computer and saveable to a disk or something. Can't imagine that the people of the post-apocalyptic world are creating new technologies just yet, just saluaging. Which is somewhat the charm of fallout. Of course they can always 'jury-rig' new things.
So main cities should be NPC factions with only gangs/guilds/clans loyal to those factions being able to hold these areas. Also, posts should exist but are freely conquerable by any though someone who fights for the Brotherhood and attains a post near Shady Springs may want to revisit memories of their Mojave chapters, just as an example. But having Enclave followers in an NCR city seems a bit mad.
I would like to see 'independent' towns that are open to conquest, giving bonuses to factions if conquered! But that's just my two pence.