so passives are a bit of a leap for Muse to implement as well as quite a change to the structure of the classes... other proposed solutions to the gunner's predicament involve complex reworks to the class system.
My suggestion is to introduce new ammo types along the lines of the new Heatsink - their primary role is a utility, rather than damage, function - and one that is delivered on reload.
Buff Ammo
loading this into a gun fully buffs it. This leaves a gunner with significantly less buff ability than an engineer but still something to go by. To ensure the gunner is still able to take advantage of their variety of ammo types, the buff should only be applied when the next clip is loaded, or gun buffs should be totally reworked so the buff is consumed by firing instead of drained over time. Not only does this make the gunner more powerful, it makes skilled ammo management and timing of reloads + buff reloads more important and rewarding.
Repair Ammo (Gel Clip)
loading this into a gun fully repairs that gun. Which is pretty powerful - but it only works on guns, is basically exclusively viable for gunners and reloads do get slower on damaged guns anyway.
Coolant Clip
this is to Heatsink what the Extinguisher is to Chemspray... removes all firestacks on the gun.
Autoloader
This ammo does nothing special to damage or projectiles - however it has halved clip size and unloads from the gun really quickly (maybe twice as fast); its primary purpose is to allow the gunner to rapidly deploy the correct situational ammo as they come into combat.
These would be pretty powerful; the first 3 situationally even more powerful than Engineer tools considering no repair cooldowns are involved. However I think that's about right. It means the Gunner would take its rightful place as the best class to have dedicated on guns. Gungineers would remain powerful and viable for their versatility but we'd no longer have the current silliness where a buffgineer can beat a Gunner on DPS as well as repair power.
You'll note that unlike heatsink, I haven't included any effect on damage, projectile speed etc. on these ammunitions. Mostly because I envisage that you wouldn't actually want to fire them, just use them for their utility. Maybe they would need some penalties to combat effectiveness to prevent them being too strong or overshadowing the gunner's old set of tools, or even a 100% clipsize reduction to force an instant reload.