Why not be able to take control of simply ONE square on the map? I mean, like go in the encounter, use some item, like.. the G.E.C.K. then you will have a quest in your pipboy to kill all npcs on your square, you must then go to worldmap and travel around for one of every enounter and eliminate them, then go back to the marker on map to the G.E.C.K. and you will soon have a couple tents (3) and a box or two, you could upgrade it by clicking on the geck that will act as a terminal blah blah blah im sure you guys know where I'm going with this.
Oh and you could raid or take over these places.