In the case of Galactic Civilizations II, an epic spacestrategy game set in space, that extra element is a design that is clearly focused on catering to the desires of the player, rather than on trying to stuff the designer's preferences down your throat. Galactic Civilizations II does indeed boast a very impressive list of cool features, but it also has that extra 'something' that separates pretty good games from Hall of Fame material.
Great games are always more than the sum of their feature sets, and Galactic Civilizations II is a great game.