I'd like to see your cities and towns have a governor that you choose from a list and assign.
The governor need not be an actual unit on the game map, but more of a statistic. The governor would have strengths and weaknesses, and you could chose him based off what you want the town to do.
Want a town to produce the tools of warfare your empire needs? Pick a governor who's well versed with industry. Need a farming town to feed your empire? Find the governor who understands agriculture the best. The choice in governor could also dictate how any automation for that town prioritizes its production.
This role could alternatively be filled with non-combat heroes, who apply their bonuses/penalties to whichever town they are in.
Either way the governor or hero could be assassinated, causing the town to fall into anarchy, halting production and trade until a new governor is appointed and regains control, or after so many turns pass.