Personally, I love having the battle scars on the hull of my ship. I don't mind that it messes up my paint job, and I don't mind that there are unsightly planks in the captain's cabin...
However, what I DO NOT like are wheels with those puny sticks as turning points. No thanks. Same with my capstan. I'm supposed to get splinters while raising my anchor from these 1x1s? Get out of here.
In that respect, I would love to see options at the shipwright! "Repair All," "Repair Hull," "Repair Mast," Repair Wheel," "Repair Capstan."
Perhaps even a "Remove Scorch Marks," if you're fancy like that.
From the load screen, I feel like just "repair the ship" is right. You're going in with a fully repaired & cleaned up ship. If you want to pick & choose - go to the shipwright.
Let me have my hull scars AND a fully repaired mast!! =D