A couple of suggestions related to culture-flipping:
I think when a city culture-flips, it should not be automatically allowed to join the other civ peacefully, but instead there should be a pop-up asking if you want to let them join the other civ, and if you say no then their rev index increases. (Actually I have seen this pop-up for cities I've conquered, but I think that's triggered by nationality not culture, and when I'm trying for a cultural victory I often get lots of border cities wanting to join me, and it seems weird that the AI civs would just let them go without a fight.)
Also, with the popup asking if you want to let a city join your civ, I think the second option should *not* be "Disband the city", but just to say no and have it remain in the old civ, but with the rev index increasing. Then eventually they might break away and form their own civ (for example, Texas). Then if after they break away, they want to join you again and you accept this time, that should have a negative impact on your relations with the civ they broke away from, maybe to the point where they would declare war on you (e.g. the Mexican War).