An idea for the Dark zone will be to add Cleaners, Rioters, Rikers, Last Man Battalion as playable faction.
due to that you could make a territory control for the dark zone.
For exemple: A mall with some NPC Cleaner is wipedout by some Division players so the mall become to the division and the next repop of NPC is Division NPC, and conversely if the mall is full of NPC division and wipedout by player from Rioters , then the next repop of NPC will be Rioters. Of course players nearby who attached to the faction that is in the mall will be asked to defend it if they want to.
The interest of the dark zone will be multiplicated because its immersive to do that, its clearly the extension of the lore/background. The goal for each faction will be to control every area of the Dark zone, and of course it will never be because constanstly changing by players.
I know it may sounds impossible because its too much work, but maybe you can pick some idea or maybe it could give you better idea. I really like the world you created with this apocalyptic NYC, but for now the game is only a rush for stuff. You will never maintain players with this only goal.
Rush for stuff is good but we need to rush stuff for something after otherwise it does not make sense.