Its a toss up for me which is better. SMAC has some things that Civ3 just doesnt have. Take the social engineering for example. Instead of merely switching govts, you can switch between govts AND other things your society can focus on, like knowledge.... Its really cool.
Also, I wish some of the UN type options available in SMAC were in Civ3. Like being able to have atrocities other than nuking someone. (Using nerve gas, nerve stapling, etc.) Also, I wish you could have straight alliances in Civ3 like you can in SMAC, instead of just an MPP.
It would also be good if you could tell another civ to stop warring with one of your friends, like you can in SMAC.
Also, one thing I REALLY love about SMAC is the way satellites work. As soon as I can, I launch a TON of all the different kinds of oribital stations so I can really get my food/energy/shields going good in all my cities. I LOVE the Space Elevator secret project too.
I know Civ3 sort of ends at where the world really is now tech-wise, but it would be cool if one of the future techs would let you launch orbital hydroponics labs and stuff like that in Civ3.
There are some things that are in Civ3 that arent in SMAC tho. The most significant of which are culture and resources. SMAC suffers the same way Civ2 did when it comes to reasons to go to war. Some people like to declare war for the express reason of destroying an opponent, but that was never enough for me. I would always think "Man I wish there was a real reason for me to go to war with civ x." Well, with resources, I have that reason. "They have oil that I neeeeeed!" Heh, makes games a lot more interesting I think. I wish SMAC had resources.
All in all tho, its a real toss-up for me. I enjoy both games a lot. My dream game would be like a combo of Civ4 and SMAC2..... After you get through playing an epic game of Civ4, you then launch with your civ to Alpha Centauri and have to start a new game in SMAC2. That would be so cool. It will never happen, but I can always dream.....