Some are probably editor wishes too
1. Cities should not be burned to the ground so often. It should cause all hell to break out if you do this in modern times. Just think that US burned Baghdad to the ground and killed all its citizens... Don't think the world community would be very pleased of such an act. If this is not possible, make it possible to alter such things in the editor.
2. Add eras, at least the possibility to add them in the editor. No really limits either. So you could add as many eras as you pleased.
3. I wish firaxis used more flavor units.
4. Some units should have bonus against certain units: you should also be able to set them in the editor. Pikemen should have a bonus against "mounted units" but not agains offensive foot units etc.
5. You should be able to set "order of defense" so that you could use the poor units as "cannon fodder" first.
6. Better editor, it should be possible to do mostly everything in it. Add Civilopedi entries, add civpedia pics etc. You shoulden't need to alter text files etc.
7. Easy to add new civs. Just add them in the editor, add the pics and that's that...
8. Canals, as I guess many allready have wished for. No real limits either, but the longer the canal, the longer it will take and more it will cost.
9. Allies should be able to move into the same tile. So that you could send troops and defend your allies cities etc.
10. Revolutions: but better then it was in previous civ. Like the Vikings could revolt to Norway, Sweden, Denmark, Iceland perhaps. This could be set in the editor, and each city could be marked with wath kind of "new" civ it would eventually belong to. Revolutions could happen in different ways: Some cities could declare their independence, they could sue for political power (with some effect on loosing money etc, but you still had military power over them), they could seek to be part of a other civ (much like today) but then there would be an act of war perhaps. You could choose to crush the rebels, to allow them independence. All with different events.
Example: USA could perhaps revolt to: Confederate States, or even just States (with cities belonging to that state) so that Texas could revolt from US.
11. Be able to sell military gear (units) so that a civ that don't have that good panzer as Germany, could still buy them. Or they could also loan them.
12. Puppet states.
13. If you have occupied all of another civs cities, and the civ is "dead" it could awake in the future, declaring themselves independent again. Like Israel, after what, 2000 year or so, they got their own country again.
14. Nations could capitulate and negotiations will be taken of what will happen, will they still produce their own buildings etc, but you control their territory. This will offcourse only be possible if there is the possibility of a nation wan't their independence again and such.
15. Much more negotiations and possibilities. Like pacts, you decide wich parts of an enemy's land you will have, and which part your ally will take.
16. More "sense" to the pacts allready present, so that wartimes isn't such a mess, with everyone at war with everyone...
17. Resources in the sea could be used: oil platforms (an automatic port in it for instance?) and fish and whales could be used even if it was far away from your cities, you would send an fishing fleet or something.
18. Buildings should be (or be possible to add in the editor) required for certain units. Tank Factory to build tanks, Air Factory to build planes etc.
19. Buildings should have the ability to be obsolete. So that slave markets or something should be obsolete at some point. And sacrifical altar that is in the meso america scenario, could be a civ-specific building obsolete in more modern times.
20. Units that can heal other units, like "ambulances" and such, in enemy territory. Should only have the possibility to do such things, or even "hospital ships" would be needful in certain scenarios.
21. Units support cost could vary: from 0.1 gold (you would need 10 units before it really cost) to 10 gold a turn. Most needfor for scenarios perhaps. Same goes for buildings.
22. Attack helicopters: could attack ground targets (esp. tanks which they should have a bonus against, and perhaps a negative bonus against infantry) but they should be returned to a city after a turn. They should also be able to cross sea. Much like it was with planes in CIV2.
23. More terrain. Polar terrain. So that the likes of Greenland is not such an attractive to settle. And also "real" Polar terrain in north and south, so you could set up "research stations" etc.
24. Resources should be tradeable like today. But when you import for instance horses, you should be able to breed them yourselves after a while, so that horse resources pop up in your own tiles too...
25. Be able to "seize" terrain even though you do not have a city there. Such should perhaps only be possible with certain units (explorers, conquistadors etc.) So that you could claim territory in another continent long before you actually build cities there, same with south pole and north pole.
all i could think of at the moment... just hope Firaxis listen to this (as for instance Sports Internactive (boys behind CM) do) Games are for their fans really, withouth fans, there would be no game... And CIV is a great game, though it could be much better...