If I remember well, we are already able to buy ships in the market, or something like that. (Are we not?)


How about being able to buy unique ships, in the market, from assimilated factions? Or even like recruiting mercenarys? - maybe side-quest related ones. 


Remembering that some factions are more war-like and difficult to assimilate than others, they should too have more powerful attack ships as other factions have more powerful defense ships, or at least ground units, since some factions are like cave-man.