Here's my two penneth'....
I think that everyone agrees that the espionage system needs to be updated, and that the diplomacy system has so much unused potential that a complete re working is necessary.
But ideas such as the hex system would definitely be bad. I dont need to say why as others already have done but simplicity is the key.
3D fighting system would also hinder game play for many reasons.
Firstly, the same people that are arguing against micro managing cities are asking to micro manage battles instead and as Oda said Civ is a STRATEGY game and not a tactical game. Yes, military actions are commonplace in Civ and are necessary for most of the ways to win but it is definitely not the be all and end all of it.
Secondly, when the pesky Persians bring their tower of 50+ Immortals into battle would you really want to fight the same battles over and over again?
This situation will happen more in Civ 4 as the game engine will be different and the AI will realise that this is the best way to fight.
You may be saying but it could be turned off if you want but that is another problem. The sheer size of the engine that would govern the 3D fighting would be too costly in terms of percentage of overall programming ( bearing in mind that it would have to draw the terrain accurately from all the potential types and then accurately draw the units in the battle and then have an intuitive system of combat that would allow you to do all the things that an army is capable in a war) that to just be able to turn it off would waste resources that could be used for other stuff such as a better espionage and diplomacy section.
I would also like to see the Civ trait system added. The argument for Civ is that it is not a reproduction of history as we know it but as a hint at what could have happened. So to say that a Civ is sea faring or militaristic from the start based on our history is wrong. Most people play on random maps so how can a Civ that starts in the middle of a mountain range on the edge of a desert be a sea faring civ. I see it having to work based on your start position, then by your actions. But, I do agree that everyone will end up as militaristic, expansionist and scientific; so there definitely needs to be a lot of work and thought going into this.
Minor changes that I would like to see are:
Improved world map one that can be rotated cos I hate it when you start on the edge and your civ spans both sides
Improved foreign advisor screen that shows all the Civs and not just 8.
Better military advisor screen so that you can see where all your defences are not just units. E.g a map overlay that shows where all your SAM sites are or where all your coastal fortresses are. Strategy hints such as Land your troops there Sir because that city is only lightly defended
etc.
Rant over - who's next?