What I love about Alpha Centauri is that it had more than just great gameplay; the game had it's own special sort of aura to it. Everything in the game -- right down to the colours used in the start menu -- came together to give it something close to a personality.
However much I love Civ4, I feel it lacks the "special something" for me to like it as much as SMAC.
A good deal of this has to do with Bryan Reynolds' and other members of his team that have since left Firaxis (I think; otherwise Civ 3 and 4 would have shared some of the references to Western Philosophy found in SMAC). Another aspect is that of known vs unknown. We're all familiar with personalities like Alexander the Great and Stalin, as well as the major trends in history. All this leaves little to the imagination, especially when you compare it to the wide, wide world of Planet, Deirde, and Nwabudike Morgan. =D