There are lots of missing diplomacy features. If you are the suzerain of a city state you should be able to declare war against any civ that attacks that city state without get the egregious warmonger trait. In fact, such a declaration of war should not trigger a "loyalty to allies" trait. (Roosevelt would immediately like you more, for example.) All sorts of interactions between city states and other civs is messed up, especially when compared to civ5.