I play a HEAVILY modified version I made:
TECH TREE: Monarchy much easier to get. Big changes in Middle Ages: Easier to get to the sailing ships, and when you get to the Age of Sail it lasts longer, as I postpone the later Ironclad and later ships a bit. I like the Age of Sail. Redid the tech charts so the graphics work still as they are different enough to confuse.
Luxury/Nat. Resources: Horses and uranium are rarer. Nearly all resources can run out now and they run out a *little* more often (I figure tastes change, and other people elsewhere occasionally breed better horse putting old ones out of favor, etc..), *Nearly* every resource requires a tech to see it- some as simple as pottery (to see dyes for example), this ups the strengths of certain civs in certain directions.
UNITS: Upped the power of medieval navy units a bit to allow better differentiation among them and galleys. Upped speeds a bit. Aegis gets to carry tactical weapons. Catapults do NOT need roads (in my game it represents the people you send to build their catapult at whatever location they are seiging- MUCH more realistic!), while Artillery, Cannons, and all the rest need roads. Explorers AND Scouts can NOT pillage (the AI doesn't use them as they are marked exploration only, so this balances it better), submarines a little cheaper,
Balance and MAP issues: Overall research is slower so the ages work out better and last longer. Some key techs are expensive and others cheaper. The UN building costs 2x as much as default so it takes a LONG time to build and you have time to go start a war over it if you're not building it- no longer an easy win now.
Spying costs less with some missions now.
I think that's about it.