Andy's article includes reprints of official comments, from Paramount to Filmation (dated October 15, 1969), about Don Christensen's 1969 "concept paper" proposing for TAS: a training ship called Excalibur; Scotty's moustache; new characters called Tun-Tun, Stormy, Ploof, Steve and Bob; and a suggestion to eliminate Chekov and his paired cadet, Chris, in favour of finding a cadet pairing for Uhura.
Excalibur (originally proposed as 6D12 Lightly) would have been able to break up into smaller pods. It sounds like Tun-Tun was already slated to be replaced by the moustachioed Scotty - and his cadet counterpart, Stormy, was to be dropped. Steve was Spock's cadet companion, and Bob was McCoy's. There was concern that Kirk's companion looked too much like "any boy in the world", and Sulu's and Uhura's companions were not decided yet (although a preliminary sketch of the female cadet paired with Uhura is in "The Art of Star Trek" by Garfield & Judith Reeves-Stevens, so she did see further development).
From "The Art of Star Trek" - Note the pre-TMP moustache on Scotty!
Three early story outlines were "The Space Cocoon", "The Impossible Rainbow" and "Klingon Attack". Some "crab/spider" business in "The Space Cocoon" was deemed unacceptable for a kids' show, but there was an effort to boost up the educational angle of each TAS instalment from even this earliest incarnation. There were aliens called trogs.
Perhaps "The Space Cocoon" inspired the story about the pod ship of "Beyond the Farthest Star" (That ship was built by an insectoid race, and there was already talk of the TAS cadet ship being able to break into smaller pod vessels?) "The Impossible Rainbow" was about "a quiet boy" and fantasy becoming reality - perhaps inspired by "Charlie X"? There was concern there was "no real point" to "The Klingon Attack" and it needed work to draw out the interrelationships and to add an educational message.
Very cool trivia from the archives! Thanks Andy Mangels, Filmation animator/historian Darrell McNeil, and Titan!