After developing a party of about five NPCs in my crew, I was thinking it would be cool if I could assign them clothes to wear, either to give them more efficient defenses, but it would also be cool if I could give them a uniform for our group. Obviously that is more for fun than practicality, but I think it would be sweet.
If anything was implemented involving NPC clothing being under the control of the player, it would probably get abused by at least one or two pervs to have nude NPCs in their base, but this might be a reasonable sacrifice for having an army of cane-welding gentlemen wearing monacles and bowler hats.