I always thought it would be best if pilots have final call on what everything on their ship looks like. However, to compromise, the pilot's choices could include whatever gun skins their gunners purchased/won. To add to the fun, some gun skins could only be used if you gunner earned them through achievements, thus making it very clear you have a high level gunner on your ship.
As far as aesthetics, I would have to give cosmetic ammo effects to gunners. This would include muzzle flash, tracers, and particle effects.
Engineers would give the pilot the same extra choices for balloon and hull repair point skins.