I have an idea that you should put NPC's in the Ship because its a small change that will make the ship feel real and fun. Have them walking around working seems more real then i person controling the whole ship a lone with Compianions just standing around. The ship feel a bit empty and this could be something like me are used to seeing rbo BIOWARE when it comes to the little thing that make you feel like your not alone.
Having your companions move around the ship doing random stuff is indeed great for immersion(tobad roleplayers get the shaft in swtor)
Adding extra npc is a bad idea the ship is already to small for yourself and your companions.(atleast the jedi/sith ships)