wat?

Never played the game, but I enjoy watching the cutscenes on Youtube.
 
Academician Prokhov Zaharv looks neat.  

 
Oh. Wait. Wrong image.

Zakharov’s researchers fit Twilight extremely well. Gaia’s Children fit Fluttershy also due to the drives for peace and preservation of earth. Rainbow Dash is loud and aggressive, so the Spartan’s who don’t prosper unless in a vendetta would suit her. Applejack values traditionalism over advancement due to her old ways being so sound. (Aka:The Believers- “Fancy mathematics”) Rarity is Morgan Industries because of materialistic pursuits and businessmare tenacity. Pinkie can be The Peacekeeper faction, Lal is kind of a Wild Card when it comes to this game. Every single game his intial colonization efforts and personality change. Then, Celestia is Yang of the Human Hive. Mostly because the Human Hive is VASTLY overpowered if not knocked out early and Spike doesn’t fit the role.

Rule 1 of Alpha Centauri  
One does not buck with Lady Gaia. That scrawny pagan can throw mind worms at you when you’re still trying to research the first vehicle.

Twilight’s faction… Sparkle Harmonics. Suitably sciency and also the obvious.
 
Fluttershy… Caretakers? Already done in the original, though, so it feels a bit unoriginal.
 
AJ… Terra Firma? Bit too abstract, but otherwise perfect.
 
RD… all I can think of is Wonderbolts. Feels kinda meh though.
 
Rarity and Spike… unless they worked together I can’t think of what new they’d bring to the table. “Sparity Industries” certainly has a ring to it, mind…
 
Pinkie’s Party Planners would presumably have happier citizens, so free Psych bonus at the cost of Economics. Bread and circuses, if you want to be critical.

@ForegroundPony  
For the original factions? Or you mean like, new names for the pony factions? Hmm…

Titles under the pictures would come in handy.