I'm going to nominate the Daihatsu Naked. Presumably given that name because you're likely to feel the same level of embarrassment driving one as you would walking down the street with no clothes on.
Boxy design - check.
Doesn't make it ugly. See Lancia Delta Integrale.
Visible screws and bolts - check.
Doesn't make it ugly. See Land Rover Defender. Or Supermarine Spitfire...
Unflushed hinges - check.
Doesn't make it ugly. See original Mini.
Engine with no power - check.
Completely irrelevant to the looks 
Uninspiring paint color - check.
Almost completely irrelevant. It came in other colours. Colour is only one aspect of design and not a significant one, at least with cars.