There is an older game called STALKER which had (limited) elements of what you describe: autonomous NPCs which influence the game world. Even though it was limited, the NPCs just battled for control of certain territories, I always thought it was a really neat mechanic. It made the world feel more 'real' and alive.

You would see these factions fighting and gaining/losing territory throughout the game. You could chose to help them or just pass on by, but the actions progressed regardless of your choice.