That reminds me a S.T.A.L.K.E.R. Clear Sky or Call Of Pripyat games, where you can modify your weapons and outfit. Well, I dont think that could be possible in FL, but here is an idea: create an item called "Full Ship Upgrade", which can be Power Generator, Shield Upgrade, Armor Upgrade in all and additionally can have a negative cargo space (cleaning cargo space by tightening ship's systems). Or more special types. For example, ERA (explosive reactive armor) could protect from rocket damage, Power Accumulator could increase the ships power cells (without increasing its regen), or a Armor Regenerator could make your armor regenerate from, for example, reactor's exhaust or a star dust, microscopic debris, etc.
If it is all codable, of course.
REDACTED: Another suggestion: some DK equipment for sale on DK stations. Shields, missile launchers, DK thruster, some kind of DK power generator (it could be OP, but "living conditions" in Inner Core are not a child's sandbox too) and armor/shield upgrade, etc. And BTW, why Coalition uses Sirius-developed shieldgens? They should have their own shields at least (not talking about station/capships turrets, cruise disruptors, mines and CM droppers)(Seems to pedantic, if it is - ignore suggestion)