I hammered this point home pretty hard on the forums when they announced Tie Bomber and Y-wing (at least Hyena/vulture had a flavor reason for being pilotless), I recall using words like ‘lazy design’ and ‘future proofing?’ - it is nice to see it come up as a topic again.
‘Easiest’ fix is probably kit touch ups where they add a new (gated) ability upgrade to the ships, where they only unlock one new upgrade level for each relic level they push out. (So for right now, we could upgrade to level 2 and 3, and just have each level provide % stat boosts relevant to the ship in question, and probably at a healthy ship omega mat cost per level to somewhat mimic the gear expenditure of relic pilots).