I think you should definitely watch NQ Balance Mod.
Maybe choose interesting for yourself and add in mod.
I liked the idea:
1. Growth of occupied cities now set to 50% of normal rate rather than 0%.
2. 2% penalty to the empire science and culture for each city you own. So if you have 10 cities your empire will have -20% science and culture penalty.
3. Settler cost progression to 2x.
4. Cities that are captured have 25 Hit Points (was 50).
5. Scythia's UU heals 25 points after kill (was 50).
Thanks for the suggestions.

Here are my current thoughts on each of these, although I'm willing to discuss any of them.
1. Lowering growth penalty in occupied cities - I don't see what harm it would do to make this change. The challenging thing about it is how to communicate clearly to players that this change was made. May not matter in the end. I was already strongly considering lowering how angry rival civs gets about you occupying one of their cities.
2. Sci/Culture penalty per city - This sounds similar to how things worked in Civ 5. For now I'm going to decline to make this change. The downside of it is that it makes founding new cities later in the game penalize you. It was partly why the optimal civilization in Civ 5 consisted of just 4 highly developed cities.
3. Increasing Settler cost progression - Altho I'm not sure, I'm afraid this would very negatively impact the AI's ability to settle cities. That said, I'm looking closely at the civic that reduces the cost of Settlers by 50%. IMO it creates a really frustrating bottleneck in the current game where to play optimally you go through this "settler spamming" period where you play the 50% Settler cost card and crank out Settlers as fast as possible. I am considering moving this card further back in the Policy tree to eliminate this bottleneck, which would, essentially, have the same effect as increasing Settler production cost. The main thing I'm unsure of right now is if the AI is playing the Settler policy card and whether moving it would impact its ability to expand.
4. Lowering city HP after capture. - Hmm. Can you explain the rationale for this change? The issue I can forsee is that when you have a bunch of rival units from two different nations near a city when it falls, the City can end up going into a kind of capture-ping-pong because it's easy to capture a city low on HP with just a few units.
5. Lowering heal amount for Scythia kills - As you may have noticed, I haven't changed Scythia's bonuses yet, in part because I am not sure where to start. I agree that the healing on top of the extra units is a bit much. Do you feel Scythia is currently overpowered as is? If I take something away from Tomyris I'd like to give something back that is somewhat balanced, like I did with Sumeria. Maybe lowering the heals but improving the Kurgan?