Except the combat system: Hexes, territory around cities growing one tile at a time, city states, more clear tech tree (no "hidden" connections or units/buildings that need more than one tech), quantitative strategic resources, building upkeep costs, road upkeep costs (no more "spaghetti"), unique civ abilities...
I also like some other aspects (like the global happiness, policies and removal of sliders), but they are very controversial so I didn't include them in the main list.