To refine my prior, if a Squadron Commodore steps up to replace a fallen Fleet Admiral, same cooldown penalty--let's make it a multiplier of +1x for each command level a given leader is having to work at simultaneously.

Captain solely directing one ship or Admiral solely directing a fleet: Standard Cooldown
Captain or Admiral acting as Commodore in addition to regular duties, or Commodore same either way: Double Cooldown
Acting as all three roles simultaneously: Triple Cooldown

I would suggest that Commodore or similar Flotilla/Small Squadron Leader abilities gain a 1-card cooldown for each ship under that "Commander Ability's" effects, up to a maximum of six. Maybe Admiral abilities only affect his own squadron that turn, the next squadrons out the turn after that, and then any further outlying squadrons the turn after that. (Representing delays of messenger ships relaying the signals.)