I like your idea, but maybe resources should be the deciding factor in how good a product is not the level of a building. I think the quality of a resource should match the landscape and climate of a certain area.
I do have something to add on how businesses should be managed. Thinking about how the game on it's full release might function, there will be lots of noobs, but the exceptional shinobi who manage to accumulate lots of wealth might start their own business. For example Mars gets enough money to start his own money to start his ramen shop, and the village might want to get a little tax money from the poor guy. This would add an economic aspect to the kage elections since if they charge too much they get displeased voters and taxing them too little might be bad for the village since it gets no income to pay their shinobi.
I love the idea of caravans transporting resources from one village to another and the caravan being seized by a rival village or a rouge group. It gives a lot of meaning to bodyguard type missions besides just the kages getting protection.
Good job, it's a lot to think about
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