I played Civ II, SMAC, then CIV III and in my opinion SMAC is the best of the three.
First, I like the setting. There's an awesome feeling in the game. I love the alien setting, futuristic technologies and ideas. I absolutely love the quotes when they present the technologies you acquire. "Eternity lies ahead of and behind, have you drunk your fill?"...
SMAC also had movies which are missing in CIV III.
The music is awesome and the graphics are quite good (it even has a 3d map that CIV III doesn't). Some people don't like the sci-fi setting. But then, a strategy game isn't really all about the setting, it's much deeper than that.
SMAC has everything CIV I, CIV II, and CIV III have although CIV III has some new stuff like culture and map resources.
I feel that CIV III is a "dumbed down" version of SMAC in terms of gameplay. First, the tech tree has really been simplified. In SMAC, you have about 80 technologies advances which are interrelated. In CIV III, it's more like 4 tech trees of about 20 technologies. You also have more buildings and wonders (called secret projects). You can also design your own units. Tired of getting your workers (terraforms in SMAC) killed? Build some with the best armor available (for the right price of course).
You can do almost anything to the terrain with your terraforms (workers). You can level it, add ore remove fungus, etc.
In SMAC, you also have society models, which act a bit like governments but they are much more complex than that.
You also have a story with unique factions. Each faction has it's own personality. There's the faction that researches technologies, the faction that likes to build military units, etc. You can randomize the personalities among the factions if you want (so you don't know how they will act). Also, like in CIV III, each faction has it's own bonuses.
CIV III does not offer any improvement in terms of inteface or strategy elements. It's a dumbed down version of SMAC with a historic setting!
SMAC forever!