The Civ games are great, but all they seem to do between games is make tweaks to the same basic formula. I think the city-production game play element is becoming a bit outdated.
What I would like to see is a new system based upon more complex macro-management. Perhaps an option to build libraries or other basic public works in all cities by taking out a certain amount of gold for a certain amount of turns. I think it would also be nice if you can have the ability to micromanage the resource distribution of the cities so that they can improve certain works, or give their garrisoned army better training/equipment, instead of just allocating certain citizens to certain plots of terrain. Just having a city produce one thing every certain amount of turns is a bit simplistic.
I'd also like to see the game move from combat centered on single units to armies comprised of several different types of units. This way one could specialize one's army for certain things. I'd also like to see customizable units where you can modify their equipment in order to specialize them for certain things; e.g. make them more maneuverable by cutting down their defense. You could modify the formation of each military unit too; e.g. put the archers in the back behind the phalanx and put the spear-men on either side to protect against cavalry, or make the phalanx form a V as opposed to a straight line.
Instead of each city producing one unit of a certain type after a certain amount of turns you could change it so that each city can produce and garrison only one military unit, though the size of this unit depends upon the size of the city; e.g. your capital city could garrison an entire division, whereas a small peripheral city could garrison a battalion or a company. In order to improve/refit the city's unit you have to devote a certain amount of city resources for a certain amount of turns. You could also improve the military capacity of the city by building certain improvements such as a fort, a training camp, or a military academy. This would allow you to improve the units garrisoned in the city. I'd also like to see supply routes to one's army when they are in enemy territory. That would add a lot more strategy to invasions.
Well... on second thought, maybe I just want to see another turn based strategy game with completely different game play mechanics than Civ. Lol.