So, firstly, I don't see a problem with gunners being underused or underpowered. They are a single facet of an extremely complex game.
With that said, to all players that think gunners should be a more attractive option:
There are several changes that wouldn't work. The first is simply making gungineers less attractive. This wouldn't work because all it does is move the choice further into the engineer's court. When a gungineer is selected for a position there are two reasons for it. Repairability and damage. With this kind of change you're basically trying to remove the increased damage from the equation. Well alright then, let's think this idea through. Without the increased damage output the choice becomes one of repairability and general versatility versus versatility on guns. This is probably the most ironic option available because the outcome of the choice is exactly the same as it would be now. On the guns that benefit from having gunners, you'd take a gunner. On guns that don't really benefit from a gunner, you'd take an engineer, but now that gungineers aren't really an option, you'd just take a normal engineer. Your ship is now doing less damage and engagements take longer, you've also not made gunners any more prolific. This is the reason that ideas like BlackenedPies's, and to a lesser extent Caprontos's, wouldn't solve any problem.
The second would be to do anything too big. Anything potentially game breaking goes into this category. For example, things like the stamina system. Or anything asymmetric. Changes that would change the name of the game more than they would fix it. There's a lot I would like to say about changes that fit into this group, but for the sake of brevity and to remain polite to Muse, I'm going to leave it at game breaking.
The only options are to introduce changes that make gunners easier to incorporate into the rest of the ship. Make gunners easier for the rest of the crew to work around. While it's a bug, an example of this is the 90s buff on guns. When buffs last long enough for a buffgineer to keep two guns buffed throughout an engagement, it allows gunners to have both versatility on guns AND benefit from the extra damage of the buff. It makes bringing a gunner a much more attractive option. While 90s is a bit long, if it was increased to around 60s it would be long enough to last throughout most engagements. And because you can keep buffs up on a gun almost indefinitely (by rebuffing between reloads) It doesn't have much of an effect overall. The gun is buffed either way, but now you can bring the gunner and the extra ammos for one of the guns.