There was a writers strike for most of season one. A provision in the contract permitted one episode to be written for an animated show if the writer had no previous animation writing credits. So, DC Fontana reached out to TOS live action writers, to science fiction authors (Larry Niven!) and Walter Koenig (who played Chekov) to see if they would be willing to take on an episode.

As far as I know, TAS season two is the way it is because the show was canceled, but 6 episodes had already been greenlit.