We need to be careful about how this works... Currently, each role is similar in the sense that they all get two bonus tools to their respective skills. In order to keep that sort of thing, each role should get a benefit to its role, a passive. We should avoid making engineer/pilot less desirable, we should only make the Gunner more desirable. An increase to damage would definitely make it desirable as heck, but a small % wouldn't cause enough waves, and a large % would ruin balance. Perhaps...
What about a small buff to all aspects of each role? Gunners have 5% increase to rotation, ammo, reload, clipsize, recoil, and whatever else, while engies get a small increase to hp repaired, rebuilt, buffed, and pilots get a small increase to ship speed, turn, altitude change, etc? This would definitely make the gunner role viable to dedicated shooters.