JBG
Prince
I am a long-time Civ player, and am the authour of a number of Civ II scenarios. I own Civ II, Conflicts in Civilisation, Fantastic Worlds, Civ III, and C3C.
Here are the ways I think the greatest game series of all time could be improved:
More realistic exploration (native guides, &c) - larger maps. In the Victorian world, much of the African continent was still unexplored - it was called the Dark Continent. In Civ III, by map trading, &c, the entire world can be known by as early as the Renaissance Era.
Rise Of Nations-style attrition damage - when one of your units is in enemy territory, it suffers Civ II helicopter style damage every turn. One could have supply wagons, &c to counter this and reduce the effects of attrition damage for any nearby units.
The reintroduction of trade units - caravans, &c played a major part in Middle Age and Ancient exploration of the Old World.
More realistic culture - in the current incarnation of the game, there is little you can do to influence the cultural expansion of your empire, other than building things in cities - you should be able to have other forms of culture, such as Great Works (novels, art, &c - NOT as wonders), random events and TV/Radio stations. Great Works could be randomly generated events, that could give a bonus in a city for a length of time - like a localised Golden Age.
By the same token, you could receive bonuses CTP-style for the first ship to circumnavigate the globe, the first person to research specific technologies, the first people to build and improvement, and the first person to field a particular unit. In such a game, there would be far more incentive to do things - a much better sense of achievement
Changing leaders - governments changing due to uprisings, coups d'etat, elections, deaths of kings/queens, &c. Therefore, as well as an overall style (exansionist, seafaring, &c), a civilisation could change what it does and how it does it according to the style of its leader (Queen Victoria, Hitler, Tony Blair, Margaret Thatcher, Napoleon, Nero, George Washington, &c, &c could each have different traits). One could have one's spies try to assassinate a leader to force a change of government.
More realistic air untis - one could opt at the start of a game to have air units use the missions system or move Civ II-style. Also, one could set in the editor which units could do what - therefore, one could combine mission-bound fighters with more flexible helicopters and airships.
MUCH less Americanisation. Money is in $, Apollo Programme, Manhattan Project, Wall Street, the Pentagon, &c are ALL American - why not have The Houses of Parliament/Westminster Palace; the Tower of London, the Leaning Tower of Pisa, the Walls of Constantinople, the Angkor Wat, &c, rather than all this idealistic, pro-American propaganda?
A far more fluid and user-friendly editor system - more inclusion of the Civ II FW elements (such as in-editor sound- and graphic- editing, as well, perhaps, as in-editor description and civilopedia editing. This would eliminate the need to wade through countless directory files and would also reduce the ways in which one could disrupt the game 
Just my two coppper coins of the realm.
Here are the ways I think the greatest game series of all time could be improved:










Just my two coppper coins of the realm.