My first thought, of course was Sid Meier's Alpha Centauri, and the third link above discusses that similarity. However, it looks like they're making a bunch of improvements on the basic gameplay (as well as some choices I think are potentially silly, but may work out well).
- More early-game customization. It looks like you select a funding nationality, and then colonists, and so on. It's not clear whether this will be "give me Korea's cultural ability and Siam's unique building and the Maya's unique building" or more like the religion system in Civ V or "I want to start with a settler, a library once I build, and a scout."
- 'Barbarians' which are intended to be meaningful over the course of the entire game
- Combination of tech and ideology. It makes sense for the Human Purity types to not get, say, mind machine interfaces. I don't quite buy that it will actually be a 'web'- that is, say, a level 3 purity tech unlocks level 2 techs linked to it- and so expect it to be multiple, potentially combined trees, like in, say, Endless Space.
- Satellite layer. Will probably be an improvement over SMAC's satellites- which just made ICS a better plan- and will hopefully have civilian as well as military uses.
Not as sure about:
- Separating colonies by nationality. Having an ideological split from the get-go was one of my favorite things about SMAC; replacing that with "we're funded by NASA" and "we're funded by CNSA" seems less gripping. But perhaps the nationality will just be names and color, and so entirely cosmetic.
- Balance. One of the things that made SMAC a great simulation, if a worse game, was that the factions were inherently imbalanced. Turns out, being a fundamentalist theist is not good preparation for the future! Who would have guessed. Civ V had huge balance problems on launch, and I don't think those were intentional- so we'll see how this launch goes.
- No mention yet of terraforming, one of the huge draws of SMAC over Civ. My guess is that it won't make it in.