I like the idea of shuttles and having them instead of fighters, so they can be manned by an officer. Which officer, that would depend on the mission.
Giving it basic impulse drive with a small amount of shields, no ordnance and perhaps a tiny beam (for mining or other purposes, not for combat) would be enough, I think. The number of them on a ship should be proportional to the ship’s size. Also, adding a Life Pod if it’s destroyed might be a good idea.