So lots of times the AI builds a city in some place you don't want them to. And while it's totally possible to just destroy their city or capture it with your military, I think there needs to be a non-military solution to the problem.
So I suggest another set of entries in the diplomacy screen where you can offer to "buy" AI cities and convert them to yours, or give up control of one of your's.
This should be intended as a late game money sink, because cities should probably be the most expensive diplomatic item you can think of. I'm thinking values in the several 1,000's, maybe even tens of thousands.
And of course, the AI would never sell its capitol.
Some things it could use for valuation:
Population
Distance from the Capital. (x amount per tile)
Number of common structures.
Number of resource nodes associated with the city.
City level.
Number of active caravan routes.
Number of "special structures", i.e. achievements.
Probably a few other things.