Im sure anyone who has played gets annoyed how a 3 man engineer team with the 1 gunner skill needed to man the main guns can easily outgun and crazyily out-tank everyone. On top of that the gunner feels very trivial usually only needing one type of ammo to compensate for their main gun. My suggestion is to make the classes more unique.
For the captain, No engineer slot, or gunner slot, 5 captain slots.
For the Engineer, One Captain slot (for sightglass), 4 engineer slots, 0 gunner slots
For the Gunner, One Captain slot (again sightglass), 3 Gunner slots, and only a choice between a weak all around repair item (not the wrench its too good at rebuild), hammer, or fire extinguisher.
On top of that make the gunner abilities considerably better than the default ammo. Since only the gunner can use it, it makes a reason to not have all engineers.
As it stands right now firefights against teams who either drop guns and go full repairs on retreat or already have multiple engineers are considerably hard to take down if not impossible at times without the Pyramidian win combo. The problem stems from too many people working together to instant rebuild hull, making it so they constantly tank the next volley even if they loose the armor seconds later. Since with two people either pipe+pipe or pipe+wrench takes around 2-3 seconds to rebuild. The cooldown system works wonders but the rebuild system is making games infuriatingly long if after 6+ volleys of double rocket launcher barrages they still look like they havent take a hit of worth of hull damage it feels rather underpowered compared to the repair capabilities of multiple engineers/people with the tools.