May I suggest COSMETIC system as a supplement

This will be really great and will attract a lot of people too. Also in regards to the RNG boxes, it is better applied as a supplement to your game.
People dont hesitate to pay and look good .
Eg : Change Ship color, Ambient effect[similar to repair box]

 

My internal tf2 fan wants to suggest hats... Or a spy boat... Or a spy boat with hats

 

Sure! Maybe even a sticker shop / gift boxes for random collection. You know, when you are bored building your items, you can always decorate your ship.
For the ship changing colour thing, I would say to only change the colour of that specific ship with it's similar colour (I don't think that was clear, let me give an example)
E.G. Say you want to change the colour of defender. You can only choose blue colours (light blue, greenish blue, violet blue, deep blue etc.).
Reason of that: We don't want confusion in ships.
I do understand though it would take a lot of code to implement this feature. Still, this is a pretty good idea!

 

I want a mint-green colored fixer, pronto!!