Atlantis, 2015 level:
To unlock level 6, “Atlantis, 2015”, get 100% in a repair on the Twin Fighter or any electronic-based repair mini-game after level 5.
Italy, 1502 level:
To unlock level 12, “Italy, 1502”, get an “Air Virtuoso” or higher rank on level 11.
Star Glider:
Beat the game to unlock the Star Glider ship. It is very powerful, but also very slow.