I guess my big issue is that if you don't capture at least one city the AI often seems like it just won't give up, even if they don't have any military left and you've got a city on the verge of capture. They'll wait until war weariness has crippled both of us, which just doesn't seem like a logical move. If I have to capture a city I don't want, I have to take a temporary happiness hit, and it may hurt my diplomatic standing with other civs while also permanently weakening the civ I'm at war with, which I don't necessarily want - it could make them a juicier target for someone else who then becomes a bigger threat later on.
There just doesn't seem to be any winning move against a stubborn civ other than conquering them completely and dealing with the backlash from the rest of the world. Anything else just hampers your own progress for nothing, unless you grab a really nice city but that's just going to make everyone else dislike you.