I have some suggestions:
1. Each player from the dark world has a red username, and each light world player has a blue username. Players cannot PvP other players of the same side. Undifferentiated players have the standard white name, and can attack and be attacked by either side.
2. Zer0 mentioned classes, I suggest each class has permanent active effects associated with it, e.g. spies' usernames appear as the opposing team's colour to them, and they have a five minute 'grace period' after using a portal into the opposing hub before the alert is sounded. Scouts would have speed and leaping permanently, etc. I suggest that there be a guildhall for each class, where a player should go to choose a class. We could do this with command blocks eventually, and using the guildhall would remove all active effects and give the effects of that class to the player.
3. Following on from my Light/dark wars, we could stage missions and games in the wilderness. Spies and scouts could report back to their teams about the other side's activities, and could storm/infiltrate the other side's castles, etc. One Idea I have is to give one side a day to build a defendable fortress, and have the other team attack it the next day. The defending team would have to kill all of the attacking team to keep it safe, and likewise the attacking team would have to kill all of the defending team to claim the fort.
4. We could reward players for taking part in missions. We could award points to players for helping with conquests or construction projects in the wilderness. If each player had a house in the housing district, they could use points to expand their house, or add new features. Both sides could try to get freelance players in the wilderness to support them, and could reward them with items.Basically, both factions would try to gain control over areas of the wilderness, and could bribe small factions or freelancers to help them.