I think one of the most disappointing moments in my gaming history has been while playing Medieval II: Total War. Playing as the Holy Roman Empire, the Pope decided to excommunicate my empire. After many failed attempts to take out the pope from within, I sent an army across Italy and took down the Vatican. A turn later the Vatican army respawned with a new pope elected. This cycle continued for a while until I gave up.
So many strategy games seem to focus a lot on war (or assassination) when dealing with politics, and even then seems to have little actual consequences to actions undertaken other than wiping out entire civilizations.
I think Afghanistan '11 has been one of the only games I’ve ever played that handles a political situation with the necessary consequences and focus. Anyone know of any other strategy/war game/something that does something more than just the option between ignore and kill?