well... over time ships would be tested and improved...
for example Han Solo's ship is (implied to be at least) far faster than others of her class
and the Serenity is, while not necessarily better, more personalised (who else can do a Crazy Ivan?)
so maybe as a ship gets older/spends more time in ur fleet, it gains stat bonus on whatever it's used for most (either passively or via upgrades) but slowly decrease in other stats to show degradation....
perhaps a shogun 2 total war style dilemma system where you have a chance to upgrade one of ur ships with a speed boost at the cost of flux capacity or something or other. Basically custom hull mods that stays on the ship permanently but cost no OP and can only be obtained in special occasions (such as random chance)