I’ll admit (again) to a bit of clickbaitiness in this title, in that both these games have a fair amount of depth and I haven’t explored either deeply enough to know where that depth taps out. It’s possible that Alpha Centauri is a better game at high-level play that I’m not aware of.
Here’s the thing, though: I’m not gonna find out. I don’t care if Alpha Centauri is really great at high level play, because it’s a boring slog on Specialist (difficulty 2/6) and so far as I can tell there’s no particularly good counter to the Human Hive infini-base strategy except to rush them down before they can get it going, which absolutely requires you to start within easy attack distance of them. The game has a bunch of weird, fiddly micromanagement with unit equipment that I’ve always ignored as much as possible because I’m creating dozens of units and don’t want to futz with exactly which gun each of them is holding. The differences in behavior between AI factions vanishes even on Talent (difficulty 3/6) as they all become obsessed with killing Player One even if their faction is supposed to be angled towards a diplomatic victory.
Making effective AI and balance for a 4X game is hard, so I’m not super surprised that Alpha Centauri hasn’t exactly executed it perfectly, and Beyond Earth isn’t perfect either, but it’s better. Gone is much of the irritating micromanagement, and instead the game relies far more heavily on macromanagement. We’re playing a turn-based 4X, not an RTS, so this is a good thing. The number of factions is effectively down to just three, and they all share the same starting units, only diversifying in the late game, and none of those factions is capable of gamebreaking tactics like the Human Hive megacity or the Gaian free worm military (both of which can, in theory, be accomplished by other factions as well – in fact, the megacity is the easiest way to win as most factions, which means it doesn’t even serve to be emblematic of a specific faction).
It also helps that Beyond Earth looks nicer. Graphics hit some serious diminishing returns about a decade ago, and Half-Life 2 (released 14 years ago in 2004) looks closer to modern graphics than it does to the original Half-Life (released 5 years before that in 1999). Poor art direction can certainly still result in some hideous games (the Brown Age of FPS gaming mostly looked awful despite the graphical horsepower backing it up), but there’s no denying that the baseline for game appearance has been brought up and that this improves the experience. Likewise, good art direction can save some older games (StarCraft still looks fine despite having pretty comparable graphics to Alpha Centauri), but Alpha Centauri didn’t have that. It had the right principles for good art direction, with different factions looking distinct from one another and the terrain changing as it was terraformed, but it all looks like an ugly mess.

Of course, graphics aren’t a part of gameplay which means that they have no bearing on whether or not Alpha Centauri is a better game than Beyond Earth, even though they do impact the overall experience. And if we’re going to talk about the overall experience, then obviously we need to talk about the element of Alpha Centauri so strong that people still talk about it to this day: The ideologies. Each faction in Alpha Centauri is a distinct ideology with a fully fleshed out philosophy backing it up, delivered through quotes from the faction leaders attached to technology unlocks or secret project (wonders from Civilization re-skinned for sci-fi) completions. You can listen to them all on YouTube and you should totally do that. None of them are unreasonable caricatures, and all of them are distinct and easy to remember from the others (well, except for the expansion factions, many of which are just slight alterations on the original seven, but I’m mainly talking about the base seven). It is an excellent example of just how much depth you can give to a setting through just a sentence or two of description or dialogue here and there, Magic: the Gathering style. Alpha Centauri’s sci-fi concepts and the different factions’ varied reaction to them remain the gold standard for philosophical depth in an interactive medium even decades later. I still discuss the different factions today, and some of the jargon for its sci-fi concepts has made its way into my standard vocabulary (example: “if your solution to a societal problem is ‘genejacks,’ you are probably the bad guys” is a phrase that’s useful in more situations than you might expect).
Here’s the thing, though: Those YouTube videos of the quotes that I linked above are just as good a means of consuming that content as actually playing Alpha Centauri. The quotes are fantastic, but the game they are attached to has aged very poorly, to the point where listening to the quotes by themselves (perhaps while playing Beyond Earth in another window) is a better, faster way of consuming the content than playing through the clunky, ugly game they’re attached to. Those quotes were intended to enhance the game, to give it lore and philosophical depth (and even a canonical arc to the game: the Gaians defeat the Spartans by surprising them with mindworms early on, Morgan Industries, the Human Hive, the Peacekeeping Forces, and the Lord’s Believers have midgame quotes but not endgame quotes, which implies they all bit it somewhere in the midgame, leaving the final confrontation to the University and Gaians) delivered in small fragments packed hyper-dense with interesting content. They were wildly successful, far more so than the game to which they were attached, which is little more than an early-era Civilization clone.
Having only passing familiarity with Civilization games before IV, it’s hard for me to say whether it draws more DNA from the previous Civilization II or the soon (ish) after released Civilization III, but the lack of any kind of cultural victory or unique units indicates more Civ II DNA to me. And listen: Civilization games have come a long way since Civilization II and III. Each game has refined elements from previous games while also introducing new ones. That’s not to say that the latest games are always better, because sometimes a new mechanic is introduced in an unrefined and shoddy manner, which can harm the overall experience more than the refinement of older mechanics improves it, but the general trajectory of the series is still upwards (even though the exact game-to-game ranking varies based on which features you care about). Civilization V is a better game than Civilization II, and a game that is basically Civ V wearing a space hat is a better game than one that’s basically Civ II wearing a space hat.