However, my definition of what can be considered a game is also quite broad, and Obra Dinn clearly has an interactive game loop so I think it counts.
I didn't play civ2, but what fresh ideas did alpha centauri bring?
There was the ability to do unit customization (which actually could get a bit overwhelming to teenage me), which came from other 4X gamee set in space I guess.
Another thing is that Civ 1/2 didn't really have very strong differences between nations gameplay wise (if you played as them, enemy AI is a different story). That really started with Alpha Centauri and its ideological factions being partially represented by their gameplay strengths and weaknesses. The way it balances an implied a grander sci-fi narrative through these ideological factions and quotes from their leaders on the one hand, and gameplay mechanics affecting how these factions evolve with the development of new technologies on the other was novel and hasn't really been equalled since imo.
For example, I think Lukas Pope is a good modern example of single author creating really unique and novel games. Civ 2 and Alpha Centauri on the other hand are more like good examples of fresh ideas being injected into a series under new leadership.