TL;DR: RPG's Need a Player character who is a unique and verry werry special little snowflake.
Given that you can actually see your player character's portrait, can name them, can move them personally about on the battlefield (sort of), you can only directly control they ship they are in, and I assume there is going to be some type of storyline or something in the campaign you are going to have to make lasting decisions in, its important that they have their own character and be useful and distinct.
"I have trained for years to be a captain of an advanced starship capable of FTL and all that implies, and I am in direct control of it, and its functions, and yet compared to this newbie ensign engineer, I contribute nothing to my ship at all"
Doesn't make much sense does it. Your captain would have some sort of command training, and a skillset to match. While you could say "Its a videogame, it doesn't have to make sense." And you're partially right, at the same time to go against what people will subconsciously expect to be logical, can rub them the wrong way and sour the experience.
Also, to make officers directly reliant on YOUR level for acquiring them and leveling up, strips them, as well as the pc, of any distinct character. They only get better when YOU the captain get better and decide to throw them a bone. So rather being a distinct and independent person that progresses and improves on their own through time and experience, they're just a nameless appendage of the pc. The real heart of an RPG, even a spaceship RPG where you only ever see ships and an occasional portrait, is to draw the player into the role they are in, to make them BELIEVE, if only just a little. To care, even if only slightly, about their character, officers, ships, and colonies/spacetations.