It seems to me that the AI has a couple of diplomatic options that the human player doesn't. the game really needs a "warning" option, when a neutral factions soldiers are wandering through your land you need a "transgression" option. it's really frustrating watching them come, knowing what they're up to but if you attack first the pope is mad at you! It'd be nice to have a diplomat go out and tell them they're entering a world of pain if they come any nearer.
It's quite annoying when you get the runt of the faction litter come up to your army and say "give us money or we attack" when you know that 5 turns after their attack they'll be wiped out. so it's also a bit odd that the AI can "firmly refuse" you but you cant do the same.

Does anyone know how your reputation is worked out? When I send out a diplomat mine often comes up as "Very Untrustworthy" but I have never broken an alliance even though plenty have broken with me.