There are reasons why conflict towns didn't work, the big one was once you managed to turn a town from one of the mighty clans like the saints (If you could that is.) there were no real advantages for your faction or clan. Turning the towns involved lots of boring repeat missions and the general loot from resources wasn't that great at the end of day. Fallen earth actually did conflict towns very badly, however clan wars despite the bugs were actually quite fun.
There was a problem of loyalty to clan or faction in fallen earth as most clans were mufti-faction and confused the whole issue with conflict towns. Lots of mistakes by fallen earth which shouldn't necessarily drop the idea or concept for this game. Conflict zones could work over truly rare resources and there is enough people playing to make those areas unsafe and if the developers are clever enough they could work it that the good stuff only spawns during prime times. If it were me I'd have an old saw factory in one corner of the map and an old cemetery/slaughter house in the other. Maybe more areas or smaller sources of rare stuff to fight over.