Ooh, I like this! This is another way CiVvI (I'm totally going to write this a different way every time now) is going to ask you to make adjustments to your situation. Its no longer, "Hey, these city states are the best city states", or, "Ally with every city state if you go patronage, no reason not to", but instead, "Ally city states based on what your empire looks like."
If you go heavy science, you'll get more benefits our of a scientific city state, and if you go heavy gold, you'll get more benefits out of an economic city state. I think that's a lot better than a flat benefit for whoever owns it, and adds a bit more strategy and flavor to the game overall.
You also don't need to complain anymore about city states marching their units in the water while the enemy is attacking them, which is cool. Or if you do, you can always go, "hey, should have had more gold!"