I don't know how complicated it would be to do this or not, but...
Instead of having a static 'This is a hangar, it's 10x6 squares', I would like to be able to draw a hangar (similar to drawing a table in Excel). That way, a fleet carrier could have a very, very large hangar area, and an escort carrier could have a smaller one. A cruiser could have a small boat bay, etc. Assign each type of craft a footprint, like 2x3, 4x5, etc. That way you can optimize a carrier to be a carrier, or allow a cruiser to have a interface craft (one could also use cubic meters, but that might be complicated).
As for types of small craft: Interceptors: Space superiority types Bombers; Larger ships carrying specific anti-ship weapons, less effective against fighters Multi-Role Fighters: F/A-18's in space (can have different loadouts for different missions, but isn't as good as specialized small craft). Shuttles: Small personnel transfer ships Assault Shuttles: Like a shuttle, but larger, armed and armored, intended for assaulting a ship or planetary facility. SAR: Search and rescue craft, again, like a shuttle but specialized for recovering small craft (which would be flying off ballistically, and probably pitching and rolling), or life pods. would need additional life support, a larger airlock, probably some kind of robotic arm to catch whatever it is they're retrieving.
Drones: Attack Drones: A smaller form of fighter, serves much the same role but doesn't require a pilot (instead relies on telemetry from the launching ship, with all the vulnerabilities that implies). Would have comparable effectiveness, but probably more costly. Could be very easily subtyped.
defense drones: As with attack drones, small, fast, pilotless. But instead of carrying anti ship weapons, would carry counter missiles and laser clusters to defend the launching ship from enemy fighters and missiles. Also, easily subtyped.
Recon Drones: Larger than attack or defence drones, but with much greater endurance, a large sensor array, and a large amount of electronic countermeasures to try and reduce the effectiveness of enemy sensors.
Repair drones: As above, but specialized to repair external segments of hulls.
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