It's hard to know exactly what the "units" in Civ 4 (and previous games) are intended to represent. But I think the game would make more strategic sense if the game moved away from the "stack dueling" concept, and into something that represented the way actual armies were put together. The system as it's set up now is more based on micromanagement than strategy.
I wish you could put together field units more like real life armies - made up of strategic units that combine arms. Even in ancient times, nobody went to war with just swordsmen or just artillary. Armies were made up of collections of units that fought (from a strategic point of view) as one.
Of course there were notable exceptions, such as the Mongol all-horse armies, but those should be treated as special units rather than the rule for all combat. Generally, there could be a standard division setup (using whichever types of each class you currently had the technology for.) And you could "design" special-purpose divisions to emphasize one aspect or another. For example, add a few more artillery, or make it more heavy-infantry dependant, etc.
Each "division" would be several times more powerful than the current units in the game, but you couldn't "stack" two of them in the same square. This (roughly) represents an ancient army's inability to over-forage an area, and a modern army's need to spread out due to area-effect weaponry. Instead of one graphic substituting for all the various units in a stack, the graphic could consist of three different units, say, infantry, calvary and artillery, with the size of each icon proportional to the relative strength of each component.
Instead of "stacks of doom", a divisions could "support" the divisions in adjacent squares (including just those touching on corners.) This would help represent geographic bottlenecks. If say, there were three units in a line against one, the middle unit would attack at full strength, and the corner units would add to the attack at (say) 20% of full power. As an extreme example: if you completely surrounded one enemy division, all four armies on each side could attack at full power, and the ones on the corners could attack at 20% each - all at the same time.
This would allow for more realistic strategy scenarios; where you could control territory by setting up a "line" of soldiers; and players could partially or completely "surround" enemy forces, and attack with strategic advantage, while also cutting off an enemy's chance of escape.
Other aspects of the game could be preserved with a system like this. Early units (before full divisions could be afforded) and raiding units could be represented by special units, much cheaper and less powerful than divisions. Also, a city defense force would not have to consist of a division. It is much easier and cheaper to train garrison units than field units; you could basically just make them part of the city.
I thought the original Civ was a great game. But, personally, it's hard for me to get into a lot of the stuff that's been added since then. I hear people talk about things like "rushing to hinduism, setting up a Great Person Factory, and then culture bombing an enemy city..." etc. I suppose that is strategy of a sort, but an awful lot of it is just - well - silly. In this day-and-age, why couldn't the game evolve into something that represents real-world strategy a little better?