Another thing I noticed when playing a scenario in Civ II FW.
In Civ III, air units can't move - they're forced to use the missions system, and, as the game wasn't designed with anything else in mind

making air units move normally simply results in laughable scenarios, such as a Harrier (UK VTOL Naval fighter jet) being shot down by an archer.
If The Powers That Be ever read this, I would put to you that the air unit system be modified so as to allow air unit movement akin to that seen in Civ II. This would be useful for such units as helicopters and airships that can stay airbourne for significant lengths of time.
Another interesting (though, sadly, less likely) addition would be the ability to have leaders change every so often (representing deaths of monarchs; the defeat of Prime Ministers and Presidents in elections, &c. Each leader could have separate characteristics (like Hitler being a very efficient industrialist and (later) a militant dictator, and Margaret Thatcher being a controversial reformer).
By the same token, one could have the ability to have spies assassinate a leader, forcing a change of government.
I myself am in the process of making an extensive mod, and one feature I find to be lacking is that there is no way to find out how a modified tech tree would look, so that in order to find out how everything is laid out, you have to fire up C3C and look. It would be much simpler to, literally, click and drag the relavent icon across the science advisor screen 'canvas'.
Another (slightly more simple) modification would be the ability to add culture groups and flavours in the editor.
More thoughts.
JB