Well, I think that adding a flight deck should be more expensive for smaller craft, as larger craft could presumably accommodate an impromptu landing strip more easily.
Also, I am in favor of a cheaper hullmod to add hanger space to craft. It is not out of the question to assume that one could (at some cost) attach a docking rig for a couple small ships onto the side of a ship (again, cheaper for larger ships), that is used out of combat.
Also, fighter repair really needs a reform, as you can repair them in combat at record speeds, but not when out of combat. Fighter repair in combat, IMO, should be a quick-fix deal, and not fully repair fighters, or fully replenish the number in the wing. It should take longer if the wing is missing members, and the new members should be not at full capacity/ammo. If they wanted a better repair job or were critically wounded, the wing could always land again for more repairs. We don't want to have other wings waiting forever because the Talon wing needed 5 more fighters, but we don't want to harshly limit the repair job.