Steel and Thunder Unique Units and Unit Expansion are great. Unique units adds one unit for each Civ, including the new R&F Civs, and the designs are really good. Unit expansions brings additional units to the game like the long swordsman and galleass, each with their own ethnic design.
Historic Speed is also great as it slows down the Technology and Civics tree whilst keeping production the same. Under this mod the game lasts 750 turns which you won't mind if you want to enjoy each era.
Rule with Faith is a good mod as it includes additional policies, governments and great people. Improved Aqueduct and Better coastal cities are also good as harbours provide more food, gold and production and aqueducts provide more food and housing.
If your computer can run it Yet (not) Another Maps Pack is the best represention of the real world map with the capacity to include every civ in the game. I don't attempt this but its fun to play on the single Europe map with about 16 civs.
There are so many new Civ&Leader mods but if I had to single out one I would suggest the Songhai mod. They are a really well designed civ with a science/ river/ religion emphasis. They also have a really cool building the Karambungo that replaces Temple, and the Mandekalu which replaces knight.
Thats six mods I'd reccomend hope this helps!