The darker one is more 'realistic'. I really think that ships in space would look more like that than the "Ship in a spotlight" look that Star Trek has taught us to expect.
But most of the other shipsets that come with the game are also quite bright. The Xiati and the Sallega are the only real exceptions and they can be very difficult to spot on the system screen. So, the brighter set is better in terms of game play even if it's less 'realistic'.