You could have a government add general bonuses to the entire nation, and then have some kind of "city hall" building that would add additional bonuses on a per city basis.
That way, you could implement it so that if you have a "city hall" in a city, it gives bonuses no matter what government you have (and a different look depending on the government), or you could implement it so that old buildings are destroyed when a new government is installed (or you take over an enemy city, modeling the installation of your government). Perhaps, in this case, a wonder could be used to make old city halls automatically change to new ones.
Lots of different ways you could do it.
That way, you could implement it so that if you have a "city hall" in a city, it gives bonuses no matter what government you have (and a different look depending on the government), or you could implement it so that old buildings are destroyed when a new government is installed (or you take over an enemy city, modeling the installation of your government). Perhaps, in this case, a wonder could be used to make old city halls automatically change to new ones.
Lots of different ways you could do it.
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