I think it would be a good idea to impliment missions that are given not to individual players, but to player factions (clans/guilds/organizations/whatever). For example, if a player faction met certain requirements the faction could be given a quest to refill thier water reserves. In this example there could be several different ways to complete the quest: caravans (either NPC or other players) could be hired to transport water to the settlement, a well could be drilled, water could be stolen, ect.
This system can also be used to control PvP between player factions and make it more interested. For example, faction A could recieve the quest to stock up on ammunition and medical supplies at the same time that faction B recieves a mission to fortify thier settlement.