I normally play as either the Drones (Alien Crossfire expansion) or the Spartans. I want the University (+2 Research) and the Cybernetic Consciousness (+2 Research, +1 Efficiency, -1 Growth) around so that some of my enemies have good technology. I also think the AI is better for the Hive, the Gaians, the Peacekeepers, and the Data Angels (do well tech-wise), so I want them around. The Nautillus Pirates spread out about the planet but I can't stand ocean bases so I normally don't play with them.
My games look like this:
Hive
University
Peacekeepers
Gaians
Data Angels
Consciousness
(My pick--Drones, Spartans. If I'm playing at Transcend might go with the Consciousness.)
The Drones have +2 Indus and -2 Research, so they're impotent computer opponents (no tech) and by playing them you won't run off with the Techs and often find yourself frustrated because you have to wait until new weapons, unit types, and city improvements come available to you (-2 Research). The Spartans aren't all that special and won't run off with the techs either (+2 Morale, +1 Police, -1 Indus) and they make for impotent computer opponents (no tech). The Spartans might be more challenging to play than the Drones (that +2 Indus can be used to build lots of research enhancements).
For those of you who don't have the Alien Crossfire expansion, you can find it (free download) here:
http://www.the-underdogs.info/game.php?id=4135
(I think it's considered to be "abandonware".)
I wish these guys would make an Alpha Centauri 2, but I don't see it happening unless they can figure out a way to make it for consoles...but console players don't play strategy games.