Hi !
In comparison to AC , the nukes in civ3 are much less effective than the planet-bursters in AC.
Civ3 has not a true 3D terrain as AC had it.
No Colonization of the oceans in civ3.
Only pre-defined units in Civ3 , but surely you can mod the game....
The governments in Civ3 are not so flexible to manage as in AC.
The Diplomacy and politics in Civ3 is much less than in AC.
Civ3 has 4 different time-chapters : Antic,medieval,industrial and modern.
I personally like (love!) the civ-series , because the epic-game is just my thing. I also like the SF-scenario of AC , but only in Civ i rejoice.
In my humble opinion , buy Civ3 + Conquest and dont forget to download the latest patch , there has been several changes through the patches.
Hope this could help you.
Have Fun !