A big bugbear for me - at present, is that no matter how much damage I do to an AI player, he'll never back down from a war (apologies if this has already been mentioned or is being implemented).
For example, I'm quite a cautious & defensively minded player, and often I'm in a position where I'm choosing to fight a defensive war, with a comparatively small fleet of orbital defenders and fast interception ships. They're relatively able to carve through anything my opponents send at me, but no matter how stalemated the war, or how many ships and troops I'm obliterating, the AI will never accept peace, because their "military strength" is greater than mine.
What I'd like to see is a peace modifier for quantity of military power destroyed during a conflict. To avoid this being OP, I'd prefer to have this cut out when the peace deal reaches White Peace (frankly, if I'm fighting a defensive war, I shouldn't be able to take much from the enemy) - but this would allow a mechanism to avoid the eternal war situation, where I can't end a tedious war without going on the offensive, something I'm not always willing, or capable of doing.