This may just be the silliest idea ever: Why not having a gunner skill that is actually a gun?
Something like a short range, raycast based blunderbuss with a long cooldown, that deals little damage, but gets a huge bonus if you are very very precise (as in hitting the subsystem itself dead on).
This way a gunner could contribute by slightly covering the ships blind spots. I understand blind spots are important and this shouldn't devalue them, so the damage should be low and balanced with the idea of needing hawkeye precision. For instance, hitting the balloon itself with this weapon wouldn't scratch it, but hitting the balloon repair system would deal significant damage.
Otherwise, a cool Gunner skill could be a bomb he/she could drop straight down overboard.
Another idea would be giving the Flare Gun (or a version of it) to the Gunner, in the form of a handheld flare gun. Mounting it on the ship seems a bit niche and it looks to me like it would make more sense that way.
I'm not saying any of these should be Gunner exclusive, just vanilla Gunner skills. By having other skills that don't directly relate to ammunition, that can be useful while guns aren't pointing the right way, Gunners would perhaps be more interesting to have on board.
I don't know, it could be fun. Bear with me if this has been said before or just sounds really stupid.