A quick idea, how about each com a clickable ability, Recon has Jump Jet, how about:
Battle Commander
Ability - Invulnerability Field - Reduces all damage taken by 50% for 5 seconds. 30second CD
Bombard Commander
Ability - Penetrating Shot - All attacks in the next 3 seconds penetrate shields and deal normal damage to 'pop-up' units.
Recon Commander
Ability - Jump Jet - Allows the unit to Jump. 30second CD
Strike Commander
Ability - Rapid Fire - Reduces reload time by 50% for 3 seconds. 30second CD
Support Commander
Ability - Advanced Stealth - The unit becomes completely invisible to all enemy units for 12 seconds. 30second CD