To expand a little on my agents idea.
I would say the first of each type of agent would be Head. Until that one dies and is replaced by the next highest level agent, with order of recruitment being the tie breaker.
The Head Ninja (call him Shinobi?) could report directly to the Daimyo who would have the power to direct all ninja activities for a given turn. If no specific orders are given by the Daimyo (and 'take no action' is an order) then the Head Ninja has discretion. The other ninjas do what the Head Ninja tells them unless there are no orders in which case they can do as they please (perhaps with restrictions around action against clans which are not enemies).
The Head Metsuke could report to the Commissioner for Finance who would have the power to direct which cities metsuke are to oversee (except in the case of no orders etc.). Except in wartime when the Commissioner for Warfare gets to appeal to the Daimyo for the release of specific metsuke to travel with armies or apprehend enemy agents. They would then be his to control until the Commissioner for Finance (or Head Metsuke) successfully appeals to the Daimyo for their release back to oversee towns.
I'm thinking the Monks could be an independent force and report to no-one (except the Head Monk).
Maybe only the Heads of each agency get to be in the running for Commissions? Or maybe they can only be eligible for certain Commissions? Like Ninja = warfare and supply, Metsuke = finance, development and supply and Monk = warfare and finance?
Just a few ill-formed ideas. Agents have the potential to be extremely valuable to the faction. A high-level ninja is worth a few armies. So it gives an incentive for people to court the favour of the Head Ninja so he can (in the absense of over-riding orders from the Daimyo) clear the way for their armies and generally help them out - you pat my back etc.
I like the idea of Commissioners being elected but with an influence-based vote so the Daimyo effectively dominates unless everyone else is against him.
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