Commanding a ship is different from piloting a mobile suit. For one, it requires much more people to properly operate and maintain. Everyone has a role to play and the difference between a good crew and an average crew can prove the ultimate difference in battle.
Below is a list detailing which positions when operating a ship benefit from which stats.
Captain: Uses either Intelligence or Wisdom. Applies half the modifier to Operator and Helmsmen actions or maneuvers.
Second in Command: Uses either Intelligence or Wisdom. Applies half the modifier to Operator and Helmsmen actions or maneuvers.
Helmsmen: Uses Reaction for evasive maneuvers. Can use Melee for ramming actions.
Operator: Uses Shooting for all attacks.
Mechanic: Uses Mechanic's skill. Adds modifier multiplied by 20 to durability and special defenses. Repairs damage equal to Mechanics x 20 every three turns.