The other point to keep into consideration, there is a very large volume of players who only want to play as a gunner, even if they're unfamiliar with ammo types, or avoid shooting the advanced weapons, this leaves us with more gunners than engineers, and the argument of gunners doing more damage would only encourage people to fight tooth and claw to he a gunner, which would only cause more unrest in the community.
When not in a competitive a competitive match I always allow one gunner on my ship, even though I understand how much effectiveness this can loose out on, it allows my friends to lower their gunner levels, though I will make them shoot lumberjack and Hades quite often...
Pies may be onto something with gunner regen buff, the problem is since stamina release, double gunners arguing with captains that gunners do more damage is more common now, even when staying calm and reasonable, it still boils down to people wanting to be a gunner because its cool...
If gunners had too big a buff, not only would it change the game mechanics too much, making glass cannons meta but it would have a knock on effect that would effect the player base..
Obviously not everyone who only wants to play as a gunner is a bad guy, and I know a fair few very worthy gunners who know the guns and ammos inside out, Geo, ZanC, Xemko and a fair few others come to mind