Ship modification without ship modification

I'd just like to pass around a thought I had that could be an interesting tactical element for the game:

Let us assume the ships are implemented with whatever model Stardock choses (perhaps static 2-ability, perhaps extensible, or something else entirely). What about the possibility of changing the ships without actually changing the ship? What I'm leading toward is the possibility of legendary pilots and ship captains. These could be similar to rare trophies/prisoners that are at the end of deep exploration or side quests. A pilot could be assigned to a ship, and although a pilot doesn't change the (active) abilities of a ship, they grant a significant passive bonus to the ship that they pilot.

Some sample ideas:

• Captain Vexpas III, "Dynamic Shield Flux", reduces damage from energy based weapons by 50%
  
  
• Commodore Srrt'zlz, "Offensive Inertial Dampening", any damage done by ship additionally reduces victim's speed by 50% for 3 seconds
  
  
• Prisoner X177b, "Graviton Signatures", enemy ships have a small localized gravity field that can pull nearby friendly projectiles toward them
  
  
• Marvin the Hero of NewEarth, "Combat Hacker", enemy ships damaged by Marvin's ship cannot activate abilities for 2 seconds
  
  
• Forgemaster Rishlu, "Optimized Energy Trafficking" , all friendly ships in combat gain a 50% increase in energy generation (assumes multi-ship combat)
  
  
• Ribbscondelev, "Alpha Round", ship abilities activated when energy is at max deal 100% extra damage
  
  
• Lulu Leafblade, "Vital Strike", damage dealt to back of enemy ship is increased by 50%