I really like the idea of certain structure providing administrative functions in general. Going back to what I said earlier about not selecting a city like you do currently, you could move most or all of the settlement info menu to the town hall. Surplus management is very important, but not until a certain point in a settlement's development. Or perhaps add a quartermaster for surplus management and have the town hall for planning functions like the top third of the settlement info window plus info necessary for expansion, etc. This could also provide ways for colonies to specialize further. The idea is that you grow into needing the services provided by these structures. We already have some of that with the way that the tradehouse works.
On the kingdom level, there could be another structure that provides even more advanced functions required for managing a kingdom, perhaps providing advanced interfaces used for balancing resources and populations across many settlements. Call it a palace and have it make the hosting city your capital, and maybe provide local bonuses as well. You could then take this further to the empire level, perhaps as some major long term upgrade or series of upgrades to your palace, with perhaps further regional administrative structures as well. They could also provide broader ui elements, such as markings on the world/region/empire/whatever map. Or maybe you don't start counting the year number until you build a palace and found a kingdom.