More realism, I'd enjoy a more civilization simulation which is actually fairly close to what Civilization is aimed at.
However, I believe a long time ago in a previous Civ you could build in space and underwater, I'd really like this added into the next Civ in a more high tech way with our better technology and resources at our disposable this could be an amazing new aspect and way to expand the game outside its boundaries while still maintaining realism.
We do have a space station built.. ya know?
Underwater would be amazing though.
Also, I read something someone posted about adding Immigration/Refuges from destroyed cities thing of that nature, you could take a lesson from real life and in captured cities there could be damage to troops until order is restored a chance of losing control and it reverting to a new nation if your military isn't adequate compared to the size of the enemy population.
Better City/Worker governing.
Better UU/UB/Traits. Unique traits to each civ would be cool.
A way to emphasis the ancient era and how even though they were single civilization a lot of the time they were infact city states run independantly and would actually war against eachother or there is a chance of it.
Your first city could be yours after that it could be a sort of internal vassal system with the chance to have internal struggles until you research a certain tech, even in the modern era there could be a trigger or triggers to create a civil war at the end of which the country rejoins or possibly part of it seperates. (not sure how players would react though)
More accuracy for ancient era units, maybe more civ specific all the way through the tech tree, different building names for different civs with certain tweaks to how they operate, kind of like UB's now but a much broader.
Possibly the ability to create your OWN civilization, the ability to possible go into religion more even though I'm not religious it would be cool to be able to found your own religion and have different choices that you decide on for that religion actually effect it and your civilization in different ways.
More in depth counter intell, maybe a form of mis-information. I think the espionage aspect could really change the game.
This may be far out there but this was a tactic used in ancient times.. Tunneling to bypass fortifications.
A empasis on the early stage of man would be cool, instead of just going strait to states run by governments you could start as tribes with simple tools and gradually build at a slower pace then we do now.
Use some of the new technologies coming out today for techs and units, they are working on all kinds of cool things for troops these days, unmanned aircraft, robotics things like that, there are concepts for space weapons we already have, one is something along the lines of well I can't remember the name it's like thor or something but I know thats wrong.. anyway, it's a device that holds huge metal polls in space and your able to target a city or area and when released the steel pole falls to the earth with such force it's like dropping a man made meteor, and that isnt fantasy thats real life they have it designed.
You could go science fiction and have a chance to discover an alien craft or tech, or be visited.. that would never happen but it would be soooo coooool
More emphasis on slavery and how it actually works, regardless of your ehtical view slavery was a major foundation of ancient times and right up until modern times. In ancient era it could be argued one of it's founding pillars for civilization.
I think different tech paths that you "COULDN'T" change or cross over from without some kind of trading from another civilization. For instance you start with 4 options for different starting techs, one is more Aggressive, one is more Builder, one is more, Cultural, .. you get the point.. you could have distinct paths that aren't easy to move across.
You could also do things a totally different way concerning technology which my be more accurate, in order to learn a new tech you have to have the resource first or the need first, meaning before you learn how to work bronze.. you have to have a copper source within your border. Thats how it worked in real life, you didnt learn how to craft bronze and "THEN" discover bronze it was the other way around. To build seige craft or buildings of a certain type you could be required to have certain materials, or you would have different defenses, which also ties into the different tech paths. If your in the middle of the desert you didnt build wooden buildings or weapons you molded them out of stone/mud.
I think in general a more realistic taking of how civilization progressed and the order and realism of it would be nice.
I also think they should remember one thing, all great games, all great things I would wager have one thing in common..
.. They pushed the envelope, they took a risk and went for it. They need to push the envelope to keep a truly great game.. truly great.
The expectations only get higher.