These items are mainly related to user interface and game play issues.
Right clicking on the icon box on the right in a city display should give the civlopedia entry for the improvement currently selected (displayed in the icon box). In fact, consider a more consistent change: In the city display make selecting units in the garrison box (to activate or disband), and selecting improvements in the box at left (to sell), a *left* mouse click instead of a right click. Then, a right click on anything in the city display takes you to the (most) appropiate entry in the civlopedia. This would include a right click on an improvement at left (show civlopedia entry for improvement), and a right click on a unit in the garrison box (show civlopedia entry for unit type). This would eliminate the need for the civlopedia mouse icon, as right clicking now on anything in the city display would always bring up the civlopedia for that item if it makes sense. Also, when the person right clicks over nothing, bring up the civlopedia anyway in normal mode. You could also add 3 more things. When the user right clicks on the name of the government just under the city name, it should bring up the civlopedia entry for that government, and if they right click on the gold listed just under the city name, it should bring up the commerce entry from the civlopedia. Finally, right clicking on terrain in the city radius display should bring up the terrain description box for that square.
On the Domestic Advisor screen, have the population of a city be shown as a (small) number in addition to the sequence of faces. In large cities the faces simply don't help in telling population size, but add some space between the normal population and the "extra" population (specialists) as seeing cities with extra population is sometimes useful, as in finding extra population to send to new cities for example. Also, add an "unhappy" item to the "happy/content" column. Finally, have clicking on the "Cities" label sort the cities alphabetically by name, and clicking on the "Producing" label sort the cities alphabetically by what they are currently producing. The first would make it easy to find a particular city, and the second would make it easy to find all cities producing a certain item.
The square terrain description box should close with a right click. This would allow the player to right click to see the description box and then just right click again to close it without needing to move the mouse.
After 3 versions there is still the annoyance of cities growing with just 1 food per turn. These cities grow by 1 food until they gain another population, at which point they now starve by 1 food until they lose the population point they gained and start the process all over. The game should prevent cities from growing with food production that is less than 2 per turn. Instead of growing, the city fills up its food box and granary (by 1 per turn) and then acts like a city that is at zero growth, and stays that way until food production rises to 2 food per turn or better.
When pollution occurs, do NOT remove the laborer from that square. Doing so forces the player to go to that city and "reset" the laborers on the city display so the now-clean square is used again. Instead, keep the laborer assigned to it. It will show the red shield (as it does now if you assign a laborer to a dirty square), but when the square is cleaned, it is still in use so the player doesn't have to do anything for the square to go back to normal use. As an alternative, consider "reseting" the laborers at the beginning of every turn, i.e., do the equivalent of the player going to the city display and clicking on the city icon in the center of the city radius display.
The pop-up box that shows up when a city doesn't have a aqueduct or hospital at the beginning of the turn should have a "zoom to city" option, to see the city display.
Right now, it is easy to avoid troublesome people in your cities, just starve them out. This is easy to do after capturing a city, anyone giving you problems can be starved to death. In reality though, starvation is the most likely thing possible to start a riot. So, any city in starvation should be very likely to, or automatically, riot. This forces the player to deal with the unruly in a little more realistic way. Do NOT do this unless you also fix the problem of cities in a grow/starve cycle because they are getting only 1 food per turn though.
The AI movement routines should "know" whether an AI civ wants to go to war with another civ before movement is executed. Right now, the movement routine will move into the player's civ's territory repeatedly. It does no good to complain, the movement routine will keep doing the same thing turn after turn. For example, if it finds a route through the player's territory to another civ it wants to attack, it will move units into the player's territory when it does not want war with the player. It will do this over and over. The movement routines should check, and if the AI does not want war, it should absolutely not allow its units to cross the border.
Planting spies should be much easier. *Using* them should be just as expensive and dangerous but just planting them should be easy. Now, it is expensive and likely to fail, usually with devastating consequences (war). Look at real life, spies are planted all the time and exposing one never leads to war. We didn't attack Israel when we caught one of their spies. How many Soviet/Russian spies have we caught over the years, yet it has never lead to war. For example, you need a spy to keep track of other countries' space programs. You aren't going to risk war just to keep track of the rival space programs, so you usually spend the entire game without spies except with countries you've already been at war with (and planted a spy while at war). Some actions should be with little risk (but still with an expense) while the more drastic actions of spies can remain expensive *and* dangerous. 2 additional options to consider adding: First, a civ can evict your ambassador. It does not lead to war but after some delay requires you to rebuild an embassy and start all over. Second, a civ can evict some of your diplomats (with a chance one of them is your spy). The expulsion doesn't lead to war, but disrupts diplomatic and espionage activities for some time before things return to normal, possibly with a cost to cover new diplomats being sent to replace the other ones.
When it comes to trading luxuries, the AI should be much more willing to trade luxury for luxury. It just doesn't make sense for all AIs to refuse to trade their own luxuries without extortion added when they would benefit as well. This should be true for trade between AIs as well as with the human player. Now if one trader already has many luxuries then the effect of adding one more is much greater and in that case the AIs can ask for more, but I've seen situations where the AI refuses to trade evenly when the benefit for both sides would be about the same.
Please consider adding the ability to see what movement command a unit already has. Something like the line displayed in SMAC when the cursor was over a unit, so you could see where it was going.
Please consider bringing back the engineers. It made so much sense for there to be 2 levels of workers, ancient and modern. You can rescale the times needed so engineers take no less time than workers do now (I'm not asking for an advantage). The engineers would also have the extra movement advantage they had in Civ2. If you prefer, just "upgrade" the worker unit's abilities as the game progresses if you don't want to add another unit to the game. Either way, a worker in modern times should have distinct advantages over the workers of ancient times including movement range, speed of working, and maybe limited terraforming ability, but not like Civ2 where everything could be changed. Perhaps just a plains<->grasslands conversion after a *long* delay?
I also want to second some suggestions made earlier. One being the ability to frame another civ for espionage actions, and the other idea is allowing the rebirth of new civs from the "civil war" of a large civ. This could be a better and more interesting way of dealing with grossly huge empires than using corruption to limit empire sizes..