I'll re-summarize my wish list items from months and months ago and I can't find the post, lol:
1) Civ borders negotiable in diplomacy screens. "This border stays here or we fight!" Once set by diplomacy, culture can no longer move a border (or "culture conquer" a city, which is just about the most ridiculous game mechanic EVER). Wars cancel previously fixed borders, and then culture takes over until the next peace treaty.
2) Make an option for real-time combat, a la Medieval Total War. Whatever units are in the "stack" deploy to a real-time battlefield, for the player to control directly in a live battle. Archers, pikemen, cavalry, all units are given orders where to go, whom to fight, etc., and tactics will be a greater determinant of who wins. Also when sacking a city, allow a real-time module when in single-player mode, to go on a bit of a rampage to vent off frustrations, etc. (and perhaps include an adult module for fully realistic ...pillaging!)
3) Add a richer backdrop of domestic politics. Opposing noblemen to watch our for; religious factions causing trouble; marriages to arrange between noble families to either strengthen allies or weaken opponents. This should run similarly to diplomacy, but on a domestic level. Overall success will have a modifier on base city happy caps, and so on.
4) Military logistics should be reworked: the PRODUCTION of a city should be building WEAPONS. The STAFFING of an army should be from the POPULATION. If a unit is disbanded the population returns to the pop of the nearest city, and the weapons may be sold for gold if not obsolete, or scrapped for raw materials (production hammers with a slight penalty) if obsolete. If simple weapons are assigned to simple population, you have a level zero unit (no XPs). If you want to train the unit (barracks or academies, etc.), there should be a TURN commitment to that training. Possibly 1 turn per XP, which can be accelerated with a Great Military Instructor. SUPPORT for a unit or a stack of units should consist of a food and gold commitment, whether the unit is in or outside of one's borders. When outside one's borders a unit should be considered "supported" (with a consistent defensible supply line running similarly to trade routes: connected by road to a friendly city without interruption by an enemy city or unit) or "unsupported" (supply lines are cut off). When supply lines are cut off, unit happy and healthy scores will begin to degrade, which will take a toll on their combat strength. When "support" is restored, the happy/healthy climb back up towards full strength.
5) There needs to be a means of transporting food within the empire. This can best be done by a special "food supply" specialist, which doesn't generate GP points or add beakers or gold or hammers, but rather, adds food scores to the pool of food available throughout the empire. In a food-poor city a player can then draw from the available food "specialist", either to work tiles or feed specialists there.
6) There should be more earth map options. Not simply "E18" as a scenario, but pre-create a number of earth scenarios showing the realistic outlay of which civilizations were on the earth map at different points in history, so that a player wanting to "role play" an actual leader from history, won't have to spend his first six months owning the game, embroiled in modding.
7) There should be a wider variety of resources. Tobacco, cocoa, citrus fruits, lead, date palms, chickens, yew trees (which should be required for longbows), all easily come to mind. Maps need to be more interesting than they currently are, and offer a greater resource-incentive for conquest or trade.
Those are the biggies, from what I see.