I started work on this a few months ago. My mod started as a city level mod. If you want to play it on easy just for a taste of how I am handling this kind of balance, it might help your overall project. For me, the key is to limit Sov based growth, reduce overall growth, increase city level power, increase difficulty of expanding by increasing difficulty of conquering expansion areas, take out almost all prestige from techs, add prestige from wonders and improvements that cost influence, make towns the only effective growth option for cities, reduce or remove consulates, nerf growth spells.
Basically there are a ton of imbalanced ways to grow cities. Vanilla cities are so weak it is not that noticeable. Once you start making cities able to grow up instead of getting more, you really notice the problems. Anyhow, my basic design is a good thing to look at for ideas. Let me know what you think.