Those who played this game few wipes ago, probably remember old TC system where you could attack town only during one hour per day, so based on that idea im giving my suggestion.
While everyone are allowed to pvp as a loners, only those in player factions are allowed to pvp as a team, so my suggestion would give opportunity to open these gates of fun for those who are in npc factions too.
Sow how should it work? Well we have 4 npc factions, that has value - Enclave, Bos, Vault city and Raiders. (while slavers are half faction ,and mordinos doesnt seem to be finished so for now i will count those out, after some updates maybe they could participate too). According to fallout reality Enclave and Bos are true enemies while same we can tell about Raiders - Vault city relation. So depending on which faction do you belong to, you could fight only against their enemy faction.
How i imagine the fight? Well as these factions are enemies, they should try if not to crush (real crush would not be possible) enemies, then take as better advantage over them as possible. So all npcs faction would make timed raids every some time. As these towns are visited by players, i think these raids shouldnt happen too often, so having one raid per week for one faction sounds very reasonable to me. For example:
Vault city make a raid against Raiders on monday 21:00 +2 GMT
Enclave against Bos tuesday 21:00 +2 GMT
Bos against Enclave wednesday 21:00 +2 GMT
Raiders against Vault city 21:00 +2 GMT
(as rest of the days could be reserved for new faction fights i mentioned before)
So now lets say monday came, and its 20:00 +2 GMT, and we have a message (similar to town control message). Vault city is about to raid Raiders base 00:59:00 left until begin. In this time all vault city and raiders members can come to a certain NPC of each faction which will give temporary (like in events) stuff that will disappear after end of the raid. Till timer reaches all 00:00 both npc faction members should take their positions, vault city citizens in world map over raiders base and raiders bunker somewhere in raiders base. After the timer reaches all zeros few NPCs on both faction sides (maybe it could even be some equalizer, for example vc has more members, so a little more raiders npcs spawn) spawn in raiders map (in this time vault city citizens should enter raiders base map also) and the cruel battle begins. The goal should be to eliminate all opposing forces in certain area. Let me explain how i imagine this situation:
When VC spawn after timer reaches 0, a locked caravan (cow with cart) also spawns in raiders map and it is watched by vault city raid boss, shortly - an officer. When raiders spawn after timer reaches 0, lets said raiders marksman also spawns in a room near locked locker. Both VC officer and Raiders marksman do not fight. They both are invulnerable if there are any forces still of their own side still alive (only those that are entered raiders map would count, and only 1 minute after timer reached zeros should be given to enter raiders map and participate in a raid). So after one faction defeats another they can kill their raid boss and loot key from it. The key unlocks the locker (either caravan, or locker depends on which side win) in which the prize for the win (object of discussion, maybe from vc you could loot medical supplies, from raiders 7.62 stuff or something and etc.) will be held. While all things in this event would be temporary and disappear after the end of raid, the loot gained from the losers locker should be permanent. Also there could be a little reputation boost with your own faction if your faction wins. Of course in these raids NPCs like Lynette for example should not participate, so only npcs that are in certain fight area should react. Raids between different factions should happen in similar fashion.
So i think that is all, maybe i will add something in the future, please express your opinions about this and dont forget to vote!