I think the biggest reason to make a new faction, as opposed to simply releasing extra ships, is to release a new Starter Set, instead of just expansions.
IE lets say they want a new type of maneuver - maybe a 4 bank, or a U turn, (different than a K, I'm talking a full blown U), lets say they want bounty hunters to have access to this new move - then they'd have to include a special maneuver template in EVERY SINGLE ship expansion.... OR simply release a core starter set for bounty hunter faction - and bam you save a bunch of packaging.