I also like Alpha Centauri better than any Civ game.
There are some downsides - initially more difficult to become familiar with the tech trees
- sure, the story IS great, but you don't care on the 50th playthrough
But the things I love about it -> you can really build your colonies to insane powerhouses of tech, money, or production
-> specialist citizens that actually rock, so you have an incentive to grow your colony's population beyond just working every tile
-> totally manipulate the terrain to do what you want - especially the 'water vapor comes from the west' idea, where slopes on the west side of a mountain get more rain, and slopes on the east side get less, and you can modify the terrain to take advantage of this. Rivers change their flow when the height of the terrain is modified. You can also stack terrain improvements to get enormous amounts of production, whether it be food, energy, or minerals. Rainy + Farm + Soil Enrichment + Condenser (And build it on jungle to boot)? Hell yes! The upper-tier enhancements are pretty neat, like the Echelon Mirror, you don't simply improve every square the same way, but lay out these "area effect improvements" in a wise manner to get maximum benefit. Terrain also plays an interesting role in combat, especially with xenofungus rules.
-> piece together your own units - you can put together some really sneaky stuff, especially with the "specials" which can totally transform a unit's effectiveness. It's far more interesting than using pre-defined units that you gain with technology. I can't emphasize this point enough.
-> social engineering - choose what bonuses and penalties your entire faction takes, even midway throughout the game - so much better than just "governments" - can get truly different results - stronger units? or fast-growing colonies? or better at mindworm combat - you can choose what you want, but take the downsides in other areas
-> mindworms are exponentially more fun than barbarians - barbarians just appear randomly where you have no line of sight, usually, but Alpha Centauri's mindwords breed in 'dangerous terrain' of xenofungus. You know where the danger comes from, and you respect it. But you can also social engineer to become experts and start TAKING THEM OVER AND USING THEM AGAINST YOUR ENEMIES! Mindworms also stay dangerous late in the game, you need to develop your Psi defenses and veteran units to counter them. Xenofungus is also a very interesting terrain aspect that affects the entire game. You can align your faction to take advantage of good terrain, but then xenofungus becomes poor for you, BOTH for combat, and for production, but if you social engineer a good PLANET rating, it becomes STRONG for you for both combat and production. However, there's a tradeoff in terms of other faction bonuses, and late-game, non-fungus improved squares are better than xenofungus in many ways for production.
A Civ-style game is really just the cities, the terrain, the units, and the country (which includes your cash, your tech, your faction bonuses and penalties, etc).
And Alpha Centauri is the best in ALL these aspects. (Look at how I bolded the aspects above)
My most-wanted turn based strategy game would be Alpha Centauri 2, with better AI (Alpha Centauri's isn't that hot), and with better player macros, so you can player-define automatic routines to remove the tedium of micromanaging late-game.