"The Tale of Teela" & "The Ultimate Battleground" are the 2 rarities. "The Powers of Grayskull: The Legend Begins" is not so rare (packaged with several figures/dinos).
Figures appeared with different mini-comics depending on when they were released. While the first Zodac was packaged with one of the mini storybooks (The Vengeance of Skeletor, as you mention), but Mattel kepts producing these figures during the run of the MOTU line.
Subsequent releases were often packaged with different mini-comics.
* I forgot to mention that some figures were "out" at the same time, but with different mini-comics: Blade for example - "The Cosmic Key" & "POG: The Legend Begins".