As for features, I rarely want to target individual fighters, but I do, sometimes want it - when a fighter is carrying missiles, or stands off too far for drones to auto-engage. The problem is, I can only dispatch drones by the squadron, and that's overkill for fighters.
Never needed to move my fighters around, except to use them as missile sponges. I don't think this is what you intend for fighters.
Bandboxing is interesting . . . but if I forget to include a ship in my bandbox move order, will they break formation? If I include them all in a bandbox, will they re-form? Fleets aren't really big enough for bandboxing to be required, but a lot of PC players will miss it if it isn't there.
I's like to see hangars drop. Enemy hangar variants, color-adjusted to signify their human alliegance.
I'd like to see detailed fighter control, in terms of being able to tell them to sit on close point defense, or to range out and attack from a distance, and whether to do that one ship at a time, or to split their numbers between all the ships around. (For fighter mop-up.) Being able to do that on a per-hangar basis isn't absolutely necessary, I think.
Can I recommend that you implement modules to improve shield regen, and have it commonly equipped by enemies? This might help solve the issue that shield-destruction is a neglected offense, with laser drones and energy cannons often discarded, or only one of each put to use. This would require shields to be taken seriously, not in the early game, and not in every bbattle, but often enough to require anti-shield equipment.
I think that perhaps limiting drones to automatic, close-range use, and requiring manned fighters to manually target ships for attack might be quite useful in balancing drones vs. fighters. This would severely limit the range of drones, but also permit more drone counts, as you might expect with automated systems.
