The original network airdate order is only representative of what episodes were ready to air at the time, and thus pretty arbitrary. It's also why a lot of the effects heavy episodes don't show up until fairly late in the season.
Another factor that went into it was the content of the episodes, especially for the season openers. In the first season, the network opened with "The Man Trap" because it had a monster and action and stuff, instead of being a more cerebral, dramatic piece like "The Corbomite Maneuver" or "The Enemy Within" or a humor piece like "Mudd's Women." And they led with "Amok Time" in the second season and "Spock's Brain" in the third because they were Spock-centric; they wanted to open the season with an emphasis on the breakout star character of the show.