I think that the system is good in itself indeed, but that it have some vicious problem... also i didn't have been happy with all of my games, especially the late ones, but here is a simple diagram:
Balanced battle system ----> high number of units (tendency - ask the AI!) ----> easy boring war
________________________+system simplicity-------------------------------->
________________________+conquered cities resistance---------------------->
________________________+overall power unbalances------------------------>
It's a pain to drag hundred units into each enemy towns in disorder, ok the keyboard shorcuts are happy but won't help for artillery or bombers [edit: it helps in fact], and the Civil Resistance make the mess bigger. However i have some suggestion to decrease some of its effects, beginning by applying a stronger anti-resistance ability to highest technology units? Also we could be able to do <examples> replacing resisters and random population by <shocked>, who according to the future field battles results could come back to normal or resisting again? [edit: anyway i think that C.R. is not 'in time' with movements troops, whiches aren't themselves with game time speed btw]
I believe the overall power unbalance to be a recurrent problem of Civilization, the better way to be fighted as I know would be to pump up the civilization number in a game!
Indeed i feel that or the randomness of the starting location have a good importance into this: My two last games unpleased to me, however i lost the first, and win goodly the second... the two in Emperor, the first with a half of a good starting location and a half of water, the second with more land and finally (with palace jump) a nearly perfect corruption-fitted comfortable landmass ball, attached to another irregular and average land (with FP taking effect in only one city?? my menus are bugged but well...). Not that i don't think that the diversity of situations would have to be reworked or something, but now i really hesitate to pass at a superior level, when i'm not sure to meet the badest situation but where i'm sure not to meet the worst, you will tell me: one less! But i became really suspicious looking at this diversity of conditions what could make the AI difficulty purely exponential... and i don't really think that i am the only weirdo who ever restarted a game, before to have play the Civ2 Iron Man mode that is. ;D So I have many suggestions of what does the AI be so agressive and randomly unbeatable.
First i would say it expands too fastly. Not only AIs civs trades like hell, but they are also dumb, especially against other AIs when it comes to defend! Also, the AI properly said is warmongering sided, so that some AI civs becomes fastly huge.
Second Civilization is expected to be a civilization game, so that it is not necessarily obvious that the only thing we would have to build in the game are military units. The more when war is more basic than the way of an escargot. So it is about the war system complexity again, and the way of playing at the whole game. I could have win (?) the first game, but at only one condition: never stop the war. Kill Persian. And match Babylon military Cavalry (still to be discovered) never stopping to build knights, and still i couldn't probably do it
before (before what you ask?

They declare war of course)
Third, trades and diplomacy. AI civs trades like hell, repeat. I can't really figure how they do it, how is it physically possible to reach such a trading rate and even how to measure it. I didn't finish to explore it yet. Babylon had nearly one age in advance in the first game, and they killed Zulus, Ottoman... about diplomacy, two things: the AI can form one big enemy regardless the number and the size of civs in less time it is needed to say it. So any puny lost civ from outter space could ask us to give salpeter or it declares war? O right cowboy, **** you, but, no, do not ally with my continental Babylonian enemy!! Argh too late. I'm dead. Ah ah, welcome in the world of Sunday-Circus-Civ! Treachery? Last thing about it is the way we ally with other civilizations... the Mutual Protection Pact must be truly perverted as we can't ally with more than 2 entities without every civilization declares war on us indeed.
In the other hand i don't feel it is such a pleasure to get lost in the middle of all those units and towns on each of which you have to click to verify the citizen mood every turns. Plus i hate the maneer of the AI to aim the town stupidly instead of having a good "fight".
The more when menus ain't coloured no more than our only opponent is exactly same coloured that you.
After a re-read i can notice that this talk not only about battle system in fact but as this one is quite thin it would have to include strategic conditions as well.