Right, I'm aware that the episodes are in airdate order, but... "Where No Man Has Gone Before" is not a regular episode. It's the pilot, so naturally it should come first regardless of having been the third aired episode. I'm not saying the series should be in production order, I'm just saying the pilot should come first. You might as well have some Season 1 episodes mixed in with Season 2. It's that bizzare.
Actually, "The Cage" is a part of the series thanks to "The Menagerie, Parts I & II." It would make sense to put it with the Season 1 special features. That way, when you buy Season 1, you can opt to watch both pilots before beginning the series. Putting the original pilot on Season 3 just doesn't make any sense at all. What if you don't like Season 3? You don't get the original pilot. LAME!