It seems like a strange thing to be worried about indeed. Why would Firaxis go back to Civ IV when Civ V was so successful? It will definitely be more in the vein of V rather than IV. My only worry is that it will feel too much like Civ. Alpha Centauri wasn't wildly different compared to Civ, but different enough. But Firaxis knows what they're doing, so I'm not putting too much stock in that concern.
You know, thinking about it, I think that there in some ways Alpha Centauri is really radically different from the Civ games. I mean, you're right that the core economic part of the game is the same, but there are three things that I think are really different to Civ (although I'm not a Civ expert so please correct me if I'm wrong!):
1: The native life forms. It's not so dissimilar from barbarians in Civ, or Native Americans in Colonisation, but it's interesting having them tied to geographical features (fungal bloom). Is there a similar system in civ that does this? like, do barbarian camps appear more often in forests or anything?
2: Customisation of units. I used to love this feature, although when I go back to it it always seems a little bit under-developed. I remember when I first realised that I could put colony pods on any chassis, and make a really fast moving colonisation unit, I was pretty impressed. I don't know whether it ever serves a practical function - maybe it could help to tailor slightly cheaper units that are only slightly ahead of your enemies tech level or something to add a bit of economic strategy to the military aspect. Whatever it's awesome anyway.
3: The biggest one though, is definitely the fact that there is a sort of proto-XCOMish narrative to the game. not basing it even loosely on real history allows a weird sort of through-line to bleed in through the periphery. In some ways I think it helps that there is a tight focus to what the game is doing, each game sort of ends up being a snapshot of a possible future for human development, as it is shaped by an alien environment. Honestly I wonder if that sort of thing will be possible under the Civilization brand, but I hope it is!
1. Barbarian camps tend to spawn near water and in remote areas. I don't think it's a hard rule, but that often seems to be the case.
2. The customization is one of the core parts of what makes AC different from other Civ games. It also mean't a lot more micromanagement. I expect Beyond Earth to have this, but hopefully streamlined a bit and to the point where it really matters.
3. Well, AC was set so far into the future, all the technology was theoretical for the most part. But even if the setting allowed for some really out-there technology, like planet busters, all that stuff was late game. Since the premise is colonization of a new planet with initial low resources and little knowledge of the planet, it still works mostly like a Civ game. Except with a lot of cool technology that opens up for very different strategies compared to Civ.