I added the advanced setup mod and deactivated Venice and Austria, removing them from the game. Firaxis wasn't thinking clearly when they decided that city states could not be liberated from acquisition, in my opinion.
If Venice or Austria are in the game, and especially if they are far from your starting position, they basically remove CS from the game entirely, which is game-breaking. It's terrible design and I'm so glad I was able to just completely remove those civs from the game entirely. I enjoy the game more now, because of it.
Civs like Greece and Mongolia still give me trouble if I'm trying to get CS allies (for example, if I'm playing Siam) but Greece and Mongolia don't break the game. I can liberate CS from the Mongols, and I can beat Greece at the ally game. It's challenging, but not broken. That's how it should be.