I have looked at using more skills and this is what I came up with. Not canon but food for your thought. Not mentioned below, but I usually restrict each character to one "action" per round, meaning the captain or engineer has to chose the best time to make use of their skill.
Skills in High Guard – Alternate System
Skills. The skills of player characters, if sufficiently higher than average, may have a noticeable effect on the battle. The average skill level of a non-player character in their assigned job (and hence the background level of the combat system) is assumed to be two. Higher skill levels can be useful in certain cases:
Battle Formation Step: The Fleet Commander with the higher Fleet Tactics skill places his ships in Battle Formation second. If both players have the same Fleet Tactics skill then both form their fleet simultaneously
Initiative Determination Step: The Fleet Tactics skill level of the Fleet Commander is a + modifier to the initiative die roll
Pre-Combat Decision Step: The skill level of a ship’s Maneuvering Drive Engineer may affects its Emergency Agility; subtract one from the Engineering skill level of the ship’s Maneuvering Drive Engineer, divide by two, and drop the fraction; the result is used as a + modifier to the ship’s effective agility
Combat Step: Skills that may affect combat are:
Ship’s Tactics – The skill level of a ship’s (or small craft/fighter’s) captain affects its performance; subtract one from the Ship’s Tactics skill level of the captain and divide by two, dropping fractions; the result is used as a + modifier to the ship’s effective computer level (a computer Model/5 is treated as a Model/6); the computer must be working at least at level 1 for this modifier to apply
Pilot/Ship’s Boat – The skill level of the ship’s/craft’s/fighter’s command pilot affects its maneuver; subtract one from the Pilot/Ship’s Boat skill level of the command pilot and divide by two, dropping fractions; the result is used as a + modifier to the ship’s/craft’s/fighter’s effective agility; the agility must be at least one for this modifier to apply
Engineering – The skill level of the ship’s Power Plant Engineer may affect its performance; subtract one from the Engineering skill level of the ship’s Chief Power Plant Engineer and divide by two, dropping fractions; the result is used as a + modifier to the ship’s effective agility; the agility must be at least one for this modifier to apply
Gunnery – The skill level of a battery’s Chief Gunner may affect its performance; for offensive weapons subtract one from the Gunnery skill level of the Battery Chief Gunner and divide by two, dropping fractions; the result is used as both a + DM Allowed To Hit and a – modifier for the Ship Damage Tables; for weapons used defensively (sandcasters, missiles or beams, and screens) the result is used as a + modifier to the effective USP - with a maximum USP 9 – of the defending battery when the firing unit determines penetration
Pursuit Step:
Pilot/Ship’s Boat - The skill level of the command pilot affects it agility in the same manner as in the Combat Step
Engineering - The skill level of a PURSUING ship’s Maneuvering Drive Engineer may affects its agility; subtract one from the Engineering skill level of the ship’s Maneuvering Drive Engineer, divide by two, and drop the fraction; the result is used as a + modifier to the ship’s effective agility (Note that the Engineering skill for ESCAPING ships is affected in the Pre-Combat Decision Step)
Navigation – The skill level of the Chief Navigator may also affect the ship’s escape – subtract one from the Navigation skill of the Chief Navigator and divide by two, dropping fractions; the result is used as a + modifier to the ship’s effective agility; the agility must be at least one for this modifier to apply
Terminal Step: Several skills are applicable to actions taken during the Terminal Step:
Tactics – Used by Ship’s Troops or Marines during Boarding Action Resolution; subtract one from the Tactics skill level of the Ship’s Troops/Marine Commander, divide by two, dropping fractions; the result is used as a + modifier for the Boarding Action Resolution roll; at least one section of boarders (5 Marines/10 Ship’s Troops/50 Crew) must be used in the boarding action for this modifier to apply
Medical – The skill level of the ship’s Chief Medical Officer can be used to restore crew casualties (including Ship’s Troops or Marines); subtract one from the Medical skill of the Chief Medical Officer, divide by two, dropping fractions; the result is the number of crew sections (or 5 Marines/10 Ship’s Troops) returned to duty after four turns; this action may used twice in battle – once to restore a crew section and once to restore 5 Marines/10 Ship’s Troops
Engineering – The skill level of the Chief Engineer can affect Damage Control and Repair; for each repair attempt subtract one from the Engineering skill level of the Chief Engineer, divide by two, dropping fractions; the result is a + modifier on the repair attempt