Should holding capitals be more difficult?

[Harv72b]

And what about Rome? Tokyo? Allies occupied these cities, for sure, but we never even remotes decided they belonged to us. Even your example here isn't apt. Berlin was occupied, yes, but we put it back under German control without Germany having to declare war to retake the city for some reason. Yet that historical tendancy is never (or almost never) reflected in Civ.

A basic primer--there's obviously a lot more detail to it:

http://en.wikipedia.org/wiki/Allied-occupied_Germany#Berlin

Japan was also occupied following the war, and continued to be up through 1952. Rome/Italy were sort of a special case as the nation itself turned on their leadership at the end of the war, but even still was occupied until 1947. Besides which, in each case (and even in other cases as recent as Kuwait, Iraq, and Afghanistan) the conquering nation has only withdrawn after basically manufacturing a government which subscribes to the same ideologies & will therefore remain friendly towards the departing power.

I get what you're saying--that these nations/cities were not annexed by their conquerors and were only puppeted for a relatively short time before being returned to independence (after having been set up to become perpetual allies)--but this has been the historic exception rather than the norm and has really only come to be the standard within the last 120 years. Could/should that be worked into the game at the appropriate time or tech level? Possibly, although implementing it for the AI leaders would likely be difficult (and highly exploitable).