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This is a great discussion, loving the ideas here.
Fighters vs Drones
For a lot of reasons, drones make more sense for space combat, reaction speed, G-forces, expandability. But manned fighters are just cooler and more fun - So we need fighters with a crew (however there may be a place for drones with salvage and rescue below).
I totally agree fighter crew should come from the carrier ships, and I agree, pilots should be specific crew and more expensive than the average crew. However, Walt has crew diversity as a planned feature, so I think pilots could be added along with other types of specialized crew. I do think though that normal crew should be able to pilot fighters too, perhaps with lower efficiency or restricted to certain types of fighter cockpit or both.
Fighter cost
Should fighters creation be infinite or should there be a limit of some kind? I would love to have fighters either way but I think they would be best with some limits. Fighter creation could have a limited, either with directly with money - or with scrap.
Salvage and fighters
Salvage is another planned feature. As you can see the feature talks about hanger bays that launch drones to collect scrap (leftover ship parts from battles), this is then stored in 'holding areas' and eventually converted to cash at space stations. Hanger bays on carriers could switch to building 'scrap drones' during battle (or some fighters and some drones) which would retrieve the remains of destroyed ships and fighters and store them in 'holding areas' (ship sections like hangers, but just for storage). As well as a simple graphic to show roughly how full the storage is, a value could be shown for scrap parts on each ship, and when fighters are created, they could use up X amount of scrap (depending on the relative cost of ships). If there is no scrap left, then 'team money' could be deducted each time a fighter is built.
Enough crew?
With scrap giving you the ability to recycle enemies into new fighters, crew numbers becomes the new hard limit for fighter creation. Very often destroyed ships parts will have some surviving crew, if these parts are salvaged, as long as they are from friendly ships, you should be able to add rescued crews to your roster - thus increasing the numbers available for fighters too (if you allow crew as well as pilots to fly fighters that is). More importantly, if your pilots survive being shot-down, you could rescue them too with salvage drones (this may have a better chance at survival if you use heavier fighter cockpits with denser armour.
Swapping fighters mid-battle
The ideas I've read so far seem to revolve around selecting fighters when you construct your carrier. I agree that there should be some ready-made fighters, but I'd like to choose designs to build mid-battle depending on what happening. For this, it would be good to have a number of hanger 'slots' for each ship. These 'slots' would appear on the UI when a carrier is selected, and when pressed would open a list of available fighters/drones etc to build. This way depending on the number of hanger spaces you've created, you could have various combinations of fighters being built at once, and be able to change types on the fly.
Torpedoes
A slightly more unconventional use for hangers, but one I'd love to see. With the ability to create custom combinations for spawnable parts, I'd love to see a version of the hanger bay dedicated to Torpedoes.
Torpedo hangers would be limited to a single width slot, and need to be attached to its own launch door on the hull of the ship. However, torpedoes would launch at a faster speed than fighters. Similarly to fighters Torpedoes would be made-up of specific parts including some of the same ones, but crucially instead of pilots, they would install a basic guidance system instead - this should make Torpedoes much cheaper to build, not just in terms of the crew used but cheaper parts too. With this system, you could design various custom torpedo types, and then (as above) swap between which types of torpedo you build in each bay.
Even if we get only half of these features I'll be over the moon.