There are so many things that could be done with the game. Unfortunately, most gaming companies seem to toss out a vanilla game and leave it to the modding community to add flavor. Unfortunately, mods are often a pain in the butt if you're not relatively experienced and comfortable modifying the program. The Civ franchise has become a zero-sum game. Instead of adding new stuff to old content, Firaxis seems to remove something old whenever they add something new so the game doesn't expand, it just changes.
So here are a few things I'd like to see in addition to the ones already mentioned:
1. A more detailed demographics model for cities. One thing I liked about Civ 3 is that there was a fairly detailed population given for your cities which I enjoyed knowing. It said how many people, to the nearest 100,000th, were living in your city.
2. Suburbs that could be built (or even spontaneously appear) in regions around the city, especially in unused tiles within your borders. Excess population due to starvation could be transferred to the suburbs, which would have a limited population capacity and generate commerce and hammers in that square. I always thought it odd that citizens would remain in a city that had a shortage of food, so why not move to the 'burbs?
3. Bring back the super highway improvement and make it an upgrade to railroads ... so instead of having railroads connecting your cities, you'd have interstate highways, which is more realistic in a modern environment. More commerce is generated by the trucking industry than the railroads. Plus the graphics would be more realistic to the eye, seeing interstates and cloverleaf intersections rather than railroad tracks. Perhaps a civ with a quarry could make concrete, which would make the highways available.
4. Internal migration. Citizens love to vote with their feet. If a city gets too large or citizens start becoming unhappy, they up-sticks and move to a different city. Why not? It happens in the real world. People go where the jobs are, where the food is, where opportunities exist, and even where the weather is warmer. Citizens in an old, over-crowded city might love to get away to a smaller, fast growing city on the 'frontier.'
5. External Immigration. Similar to internal migration, citizens from neighboring civs should flock to your empire if you're more advanced or more cultured than they are. Instead of just having a city flip to your side (which doesn't really happen in the real world), population from a rival can be siphoned off to your own empire through culture and tech wars ... one could even add a new tech advancement or wonder: the propaganda ministry, which acts like a magnet to draw citizens from other nations.
6. I like the idea of random events to keep things from becoming predictable. I know people who play with strict formulas don't like the idea of an uncontrollable variable in their equation, but I tend to find it refreshing. The key here is to balance bad events with good ones. Most games with random events saw 90% of them being a detriment to the player. While the game would have its usual litany of earthquakes, plagues, hurricanes and a meteor impact or two, those need to be balanced with random scientific breakthroughs, population booms, undiscovered resource deposits, etc. In addition, they should occur to the AI as well, and the AI needs to react to them. For instance, if the AI's capital is wiped out due to an earthquake, it should try to end any wars it is engaged in and try to settle matters at home.
7. Have an Alpha Centauri map. Instead of the game ending when the rocket blasts off, the game could continue as you colonize the new world. Sort of like combining Civ and Alpha Centauri in the same epic game, and techs would advance into the future (rather than just a generic "future tech")
8. Bring back variable game length. Some players like myself enjoy a longer game so that we can get the most out of it. Civ 3 allowed you to make the game like 200 or 300 turns longer than the standard game. To me, that made wars more appealing. I dislike getting embroiled in conflicts in the standard length game because it means actual empire building is going to get stifled as war weariness sets in and most cities are producing units instead of improvements. With a longer game, I know I have time for a war and can still max out an empire.