I think this would be a fantastic idea. It would really add to the realism and immersion of the game. Having a personal ship is one of the biggest perks for me. That said I do think that reorganizing the ships compartments is not only impractical it's a bit unrealistic. These ships have to be built somewhere and while they were customized to some degree I don't really have an issue with the standardization of ship layouts. I do think that certain things could be done to make them more personal. Different paint jobs, interior and exterior. Furniture, trophy's, etc. I would be very happy with some of those changes.