Had a most random thought of trying to match the Aptitudes with the Alpha Centauri characters without duplications:
Diedre Skye - StrikecraftIf SiC had an Industry aptitude and it had pollution-type hazard reduction skills, that would've been her pick. Instead she gets Strikecraft because 1) Its green like her faction color and 2) Kind of simulating her lore preference of using worms as "auxiliaries";
Sheng-ji Yang - AutomationIt is not like Yang treats people any better than drones;
Prokhor Zakharov - TechnicalSelf-explanatory, really. High Tech all day, every day;
Nwabudike Morgan - StarfaringIf SiC had an Industry aptitude, Morgan would've had it and speced for maximum exploitation. Instead he gets the aptitude that give hims the most opportunity for trading;
Corazon Santiago - WarfareReally, the Spartan lady has her pick of combat flavor here, but Warfare is the most obvious choice.
Miriam Godwinson - SmallcraftHorde of pather zealots incoming;
Pravin Lav - ManagementFor maximum officer-related bonuses similar to his extra Talent bonus in SMAC;
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Crossfire bonus:
Aki Zeta-Five - Symbiosis from Emergent ThreatsFor Cybernetic goodness;
Ulrik Svensgaard - PiracyThe Pirate is gonna Pirate;
Foreman Domai - Improvisation or Dustkeeper XOThe former if it was just the "vanilla" aptitudes, but the Dustkeeper XO would make him a lore-appropriate mirror to Yang;
Sinder Roze - Tactical or Improvisation Out of the remaining scraps, the Hacker lady gets a pick of Tactical (for flexibility) or Improvisation (cause Cyber
punk)
Prophet Cha Dawn - 
No matter what is left, it doesn't fit him. The only other alternative is for both Manifold factions to share an Aptitude so that Cha gets a freed one, and out of those two only the Abyssal one barely fits because of "attuned to something supernatural" thing.
Manifold Usurpers and Caretakers - Abyssal and/or ExotechAlien(-like) aptitudes for Aliens.