The main question left is
How to make the villages function by setting the actors, the rules, props, etc? By self-organization, NOT scripted.
Each level has it's own creature types, what they can do, and the rules, which their society follows.
How it all can be formalized so that we have a villages system.
How to make the system, where we can define all the variables (actors, actions, props, rules) and it would make a playable village?
Energy exchange defines interactions.
Creature skills and objects they can craft are the basis for villages economics.
Friendship and family relationships form society structure.
Nature and creature's ability to control weather form the basis for world shaping (aka "agriculture")
The core of the villages system is telling a story. A village starts from the designing the experience which we want player to live through.
After we know what experience it would be, we can start defining what are the unique characters, their relationships, and the experiences which shaped them, made them who they are. How and why they learned their skills to craft objects.
The experiences shaping the village we can call the village traditions and rituals.
And we need to set these experiences to happen in the village, which would form unique environment and creatures by self-organization.