Well, for example the terrain-manipulation mechanics are much more fleshed out, due to it aiming to be a "hard sci-fi" game with terraforming and xeno-biology. It even has a simple terrain-based weather model where (for example) the shadow-side of mountains have less rainfall, influencing fertility.

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.