I also encourage any RPG group that is running with their own ship to seriously consider the crew dynamics that would be taken into consideration by the captain. Simply put, everyone on a ship (sci-fi or otherwise) has a role to play, or else they are cargo or paying for transport. You don't go to sea with a bunch of random friends because they are friends. You take them because you need certain roles filled and they will pull their weight.
If you have a group where starship combat breaks out and you're wondering what do to with the people who aren't pilots and gunners, just identify their role on the ship and include an encounter that challenges one of those roles and let the rest of the crew deal with it while the pilot does his thing. Maybe an engine breaks down and needs an emergency repair, and suddenly Jayne and River have to help deal with that encounter while while Wash is trying to walk Book through through some co-piloting process...
If you have a group where starship combat breaks out and you're wondering what do to with the people who aren't pilots and gunners, just identify their role on the ship and include an encounter that challenges one of those roles and let the rest of the crew deal with it while the pilot does his thing. Maybe an engine breaks down and needs an emergency repair, and suddenly Jayne and River have to help deal with that encounter while while Wash is trying to walk Book through through some co-piloting process...