Resources:
I know I'm not the only one to think that the current system is a bit simplistic compared with the rest of the game, and is in obvious contrast with reality. A single copper mine can effectively supply any number of cities, for instance, and you can only trade one resource to one other civ. Instead each resource should be worth a certain amount of units, and "resource units" (RUs) could be traded, rather than the whole thing at once. So if each copper resource was worth 15RUs, I could use 10 for my axemen, but then trade 5RUs to Qin for 5RUs of iron to make 5 swordsmen.
If you wanted to make each instance worth a different amount of RUs, that would be nice but unnecessary. If you did, you could have a set limit of RUs for each map size, but maybe out of 100 oil RUs, 50 end up in one instance, while 10, 10, 20, 10 end up in four others.
Oil, coal, uranium: of course RUs would be needed for their respective other uses, like airports, coal plants, and nuclear plants. You might have to consider making their use grow with population size, so a pop-8 coal plant uses 1RU, up to a pop 16 that uses 2. I know it's not realistic considering how pop works in the game, and perhaps it's too complicated.
Civics:
It would be nice if some civics decreased player control, but gave extra benefits. For example, free market could increase trade even more, but then any excess RUs would be automatically traded to the highest AI bidder. You could give universal suffrage an emancipation-esque penalty, but then make it more constraining on war, such as bringing back the senate.
Units:
It would be nice if each civ had its own flavor of units. It's extra design time, I know, but it would be nice if there were at least subtle differences between an American destroyer and an Aztec one. Perhaps a number of civs could share similar flavors, like having an Asian flavor, a Western flavor, etc, to cut down on time to make this.
Expansion and conquest:
Are overpowered, considering history. Empires have a long history of not being able to hold on to large land grabs, and splintering. Some game mechanic to simulate this would be nice, and add an additional complexity to the game: the internal. What would be interesting is if only cities founded within a certain distance of the capital were considered "native land", where you would not have to worry about splintering, etc, but beyond that "penalties" would greatly increase. If I conquer, or even found, a city half a world away, I would need a very large force to hold it, even after anarchy had gone away. Civics and certain buildings/wonders could help mitigate or exacerbate these problems.
Splinter cities would start their own sub-civilization, depending on who had the most cultural control at the time of splitting, or would simply rejoin their "native land". One way to combat this effectively would be to "raze" culture, which would consist of sending troops to each cultured tile and "razing" it, but which would greatly increase unhappiness in the city, upset the offending civ, and hurt the unit, if not cause a spontaneous unit creation to fight it.
Tranfers:
Bring them back, and allow for pop transfers as well as food transfers.
Cottages and farms:
Why is it a town does not decrease the amount of food on the tile, but that tile can't be irrigated? It doesn't make sense...