Suggestion.
I did considered that actually but then I immediately remember seeing people complaining about how durable the fighters are in combat, hence I nerfed them all a couple times several versions ago. Maybe it should come with a downside too I guess?
or was it better to just give additional flux capacity instead since we have obvious weapon-to-flux inefficiency?
...
Generally I don't
think the CC-Bonus comes with a downside unless it's a really good bonus, given that it's something you're only supposed to get if you sign on with them or ally with them.
As for ideas... well you could make them cheaper. Something like using fighter craft get an ordinance point discount, if the discount isn't too over the top then it can be applied to the fleet without unbalancing things. Something like...
"Strike Craft Expertise = All strike craft have their ordinance cost reduced by 15%"
Just with a more thematic name, probably. You can adjust the percentage discount up or down as you determine what balances best and I think it'd be pretty unique, I don't remember if there's anything that gives an OP discount for strike craft.