What if; Taking a territory slotted a support "feat" onto the faction members currently holding it, nothing too special as you don't want the control of areas to change combat potential directly in pvp etc. But the feat itself could contain a desciption (of the small bonus) and of the effect it will have on your base, as an in game reference to what you can do/buy once these areas are taken (the specifics of which i'm actually not too sure of).
As for the bonuses, I thought a little something that represented the area taken, to give some flair to the capture. With the center being an obvious point of contest for all factions this would be the "best" bonus which I thought, a +5% bonus to gained XP (maybe not from quests, but just from crafting, killing etc). While other could vary from slightly better buying or selling prices, to slightly higher quest money rewards. Or just a little situational bonus like; controlling the whorehouse means that bootleggers in the area will treat you as friendly until fired upon (each new group). Or controlling the PV Factory means you can buy polymers and kevlar 5% cheaper.
Thoughts?