Personally I can't see more than surface similarities between the two games. In fact, GalCivII might benefit a bit from the immersive style of SMAC. In SMAC, while playing the TBS you were also playing out this incredible story of the transition of humanity from mortals to a form of immortality. Also, the AI leaders were really individuals, with their own personalities and ways of acting. GalCiv actually has a strong, interesting backstory, but personally, the campaign just isn't worth playing through to get the story. Also, the AIs seem to pick standard patterns of behaviour that are available to all of them, so they may be very different from game to game, but from their own previous behaviour, not necessarily from each other.
With that said, the most obvious difference is that SMAC was confined to one planet, and GalCiv features a whole galaxy. I find playing on galactic maps just more enjoyable than on planetary ones.