My apologies for the misunderstanding, but in the first post you referred to distributing points for your character. Kinda triggered a panic response.
Guess I'm still looking from a D&D perpective; a "skill" is something very different from a "feat" or "perk" in my world.
But yeah, very good idea. Since they seem to be focusing on more immersion with the FPS viewpoint, total modeling of the interior and crew-interaction, they should (imho) include a system that really makes the captain (you) stand out, something that makes him the commander. A system like you propose could create a bond between the player and his avatar, and between the avatar and the crew.
Heck, they could even create dialog referring to these traits. Maybe they could introduce a "cooking" one (captain is a bit of a chef in his spare time; allows longer time at sea) and have the crew compliment their Kaleun on his cooking.