Except for a few small details, I've got the basic new player setup complete. You name your ship and the captain on the same screen and the new captain starts with 0.1 in all but the basic science skills. The basic 0.1 Class Ships will be able to fly with just a captain on board, who can handle routine tasks, but the captain won't be able to get skill advances for positions he's covering for.
So a captain will start with 0.1 in Astrogation, but won't be able to advance that skill by jumping to new systems. Only personnel assigned to the Navigator position will be able to do so. The Captain will be able to advance Tactics and Command. This is all tentative of course, and could definitely change.
As ships get larger they will require more crewmembers, but I haven't exactly worked out how that will be in the game as of yet.
Here's a screenshot of a new ship Captain I created today.