Ok, i'm changing this (taking into account all suggestion that you provided), it's bit slow process. What i'm doing is this:
Hegemony, Tri, Pirates and Independents will all get 3-7 variants per ship. All fraction ships will have hull mode "theme". For example, all Pirate Hounds will have unstable_injector hull mode because Pirates depend on speed. At other hand Hegemony Hound have reinforcedhull hull mode and much better weapons then Pirates. And Independent Hound have frontshield hull mod.
Basic philosophy that I'm following is this:
Hegemony is kinetic/HE brute force: slow but durable.
Pirates are fast, agile, a bit outdated.
Independents are little bit techy better armed than Pirates but not good as Hegemony.
Tri are energy brute force.