In addition to ship builds you could do crew combinations as well:
Assign bands of matchmaking ranking ex- high,mid,low
For each ship [Captain]+[Crew,Crew,Crew]
example ships - [High Pilot]+[Mid Gunner,Mid Engineer, Low Engineer] or [Low Gunner]+[Low Gunner,Low Gunner,Low Gunner]
Having data from these extra matchmaking rankings could also help them with balancing too.