The problem comes to that:
-To control the boat, just click on the helm.
-To use a gun, just click on the gun.
-To repair a piece of equipment, just click on.... *OUCH* no, you can't.
That's actually fairly insightful. What if Engineering were based around, say, a single thing (like Gunning normal ammo, or a Pilot's ability to fly): Say a 100hp/5 second, 3 rebuild tool. Everyone gets this tool by default. Call it the Engineering Kit or something.
Then you get "modifications" that you can use. Everyone gets 1, Engineers get 3 (I'd switch Spyglass to an "everyone" tool here, and let people actually choose a piloting tool aside from that).
Fire Extinguisher: -70 repair per hit, -1 second cooldown, -1 rebuild, removes all fire stacks.
Chemical Treatment Kit: -60 repair per hit, -2 second cooldown, -1 rebuild, removes 3 fire stacks per use, prevents additional fire stacks for 30 seconds.
Quick Repair Kit: -60 repair per hit, -3 second cooldown, +2 rebuild.
Major Damage Kit: +125 repair per hit, +4 second cooldown, -1 rebuild.
...and so forth. An Engineer has flexibility above and beyond the average (due to a better selection of tools for the specific situation), while the Gunner and Pilot have the average baseline of Engineer repairing and a SINGLE addition to give them more flexibility in a specific direction. This flexibility might even allow for 2 gunner crews being competent at repairing and better at gunning, while 2 engineer crews are better at repairing and competent at gunning.