I'm going to go out on a limb here, but I think in Civ 4 one of the things that has really been ripped to shreds is the tech tree and wonders...
They are really quite different - less techs, and less distinct ages - i would have liked to have seen a distinct enlightenment age - with technology and wonders...There is less feel to the passage of time in civ 4. There needs to be more technologies with more units i think. What would be really cool is incorporating your own design of units and your own leader with your own traits, like you could do to a certain extent in master of orion 2 - what a classic game that was.
The combat system is wierd... I mean how can a 18-19th century company of rifleman BEAT a 20th century apache combat chopper squadron even if it is at half strength? There really needs to be a mod to negate some of these effects RE modern units versus units of an age below - they should be given a massive downgrade eg. - 100% or something like that. I'm sure one of the smart people around here is already working on a kickass realism mod. For example, modern armour should NEVER EVER lose points when attacking a medieval unit !!!!!!!!!!!!!!!!