I would like to see some more strategic possibilities when you go to war. Not real time battles, CIV is not a RTS but perhaps formations, attack with mixed armies at once, use of terrain (not only the tile you are on should count but also the tiles next to it, like if you are inbetween two mountians you should be able to hold of a large armie with a smaller one much easier, because they wont be able to attack with their full strenght). The war in civ is way to much luck and numbers.
Other things could be that resources could drain, and that you need a larger supply of oil to build tanks in 20 cities instead of 10. I am not sure that it really will make the game more fun though...
Trading produced goods might be something for the modern era. A economical victory option would be cool too.
More "illigal" activites (like the privateer), perhaps support gurillas or rebels in a oponents country, if the rebells win the will defeat that player and become a vassal to you (or at least a strong allied)
Just some thoughts, I havent read all posts in this thread so everything I have said might have been said already