If I understand correctly, each ship's panel shows both the ship and the pilot, and there is nothing special about a particular ship/captain beyond its starting Weapon/Defense value (I assume there will be some variation in numbers between ships) and the deck associated with the ship. I'm sure this must have come up in play testing, but:
a) why don't the ships have individual powers like heroes in SotM? Seems like that would increase the personality of the ship/captain you're playing beyond just their starting numbers. Right now, if I understand right, I'm mostly choosing a ship just because I want to use that ship's race's deck.
B) why can't I choose my ship and captain separately? If I want to play with Asteroid Jones piloting the Gryphon's Claw in one game, but with Two-Tail Merklos in the Gryphon's Claw the next game, that sounds even better, especially if each pilot had an individual power along with the ship so that I was really customizing the game the way I wanted it. Seems like this would increase that same personal attachment to the character they're playing that we have in SotM.
I'm assuming the answer to these questions is that it would unacceptably multiply the number of combinations that would need to be play tested, and it would increase (by a bit) the number of cards that would need to be printed. I think the increase in personalization would be well worth it (says the guy who doesn't have to do the play testing or pay for the printing).