There are many things to consider when it comes to a players ship.
In a perfect world the answer is all of the above. I'd like to get your impression on how important customization is. All other considerations aside.
Honestly, more or less dependant on the game.
For more military-oriented theme (Wing Commander, Freespace), at least they should give us an option to mess with the ship's loadout. As for the sandbox-y theme, customization should be emphasized.
I would agree Mv2000 that it would depend on the type of game.
Games like X-Rebirth, Rodina and Precursors ect where you can move around inside the ship need to have access to the ship systems where you can buy new components of fix systems other wise it lessons the point to having a ship interior.
I do like to have the ability to change the look of the ship, but I think if I had to rate importance I would like a wealth of options for ship systems upgrades and backup systems.
I would only like to design the flagships in a modular form. You know, the kinds of ships that are one of a kind, custom made.
I would prefer if I didn't have to micro the rest of the ships.