I have a lot of ideas but one that I think is essential to capturing an ancient world feel and that would greatly enhance strategies and depth to the game would be for the environment to have more effect on manoeuvrability.
For example:
Chariots should not be allowed to enter forest, or hills without roads.
Archers should have a significant minus to forest defense.
Some troops (thinking particularly of Germans here) should be able to walk across mountains - Imagine the threat to Rome posed by them!
The sea needs to be more challenging - most boats throughout this time hugged the coasts.... for a reason! With boats too shallow, the sea caused many to sink in storms and the like.... could the old Civ 3 % chance for boats to sink if ending their turn in a sea tile....(ok it was in ocean in Civ 3, but you get the idea)
In this way, further specialisation/customisation of the civs can be implemented. The Egyptians will be strong on the plains and grasslands, but will lose their edge if they fight the Hittites. The Germans will ultimately pose a threat to Rome when they muster enough Mountain Raiders. The Phoenicians will have boats immune to sea losses, or at least greatly reduced... etc etc etc.
To supplement this idea, I also considered another special building for each race that would produce a civ specific unit every x number of turns, with this being the only way to acquire these units.
One further thing to throw into my mass of unstructured ideas was the concept of a unique historical goal for each civ (ok, a lot of work would be required admittedly!!

). This goal would be an incentive to emulate the actual historical achievements of the civ you are playing and while it wouldn't win you the game, it would net you a lot of score and assorted benefits.
I also think more barbarian tribes and/or unplayable minor civs with preplaced cities would add a lot at the beginning of the game as you attempt to assimilate them into your culture.
Sorry for the random mess of ideas, I am normally much more structured when writing, but my chicken salad was stealing my attention!
