Mishouzaki's manga makes Zelda into Badass Adorabletomboy who disguises herself in a masculine manner at one point, and ends up getting kidnapped by Ganon. This sounds a lot like Princess Zelda in Ocarina of Time.
Zelda and Link are also half-siblings. It's a popular myth that Zelda and Link, specifically both the Hero Of Time and the SNES Link, are siblings.
All three of Shigoto's manga have Link with inaccurate hair colors. First he's a redhead, then a blond, and next he has pink hair; these are all the same Link by the way. Link was made into a blond for A Link to the Past and has been so since, and the in-game sprites show Link with pink hair due to graphical troubles.
Ass Pull: Link having Volvagia as a pet when he was child, even though during the segments with Link as child we never saw Volvagia at any point.
Although it could be seen as a "What If?" dream sequence if he had adopted the dragon isnstead of leaving the poor thing alone.
Base-Breaking Character: As if Sheik didn't break the base enough in the canon game, the manga interpretation of Sheik breaks it more. Because Sheik is "his" own consciousness in Zelda's body, rather than Zelda doing the job by herself, Sheik is liked and disliked for that same reason.
Ho Yay: The writers apparently took the fact that Ricky was a male kangaroo with a pouch and ran with it, having him gushing over the Chosen Hero, oozing admiration at Link's sword skills, and openly voicing his disappointment at the possibility of Link having a female love interest.
Four Swords - Akira Himekawa
Foe Yay: Shadow and Vio, especially since Shadow states he really did consider him a friend and actually seems hurt by The Reveal that Vio has lying to him about joining him. There's also at least a hint of it with Shadow and Zelda.
Take That, Scrappy!: Unintentionally, this manga gives plenty of this the American haters of Tingle when Vio beats him with a sledge hammer, and later when he complains about being left out of the finale of the manga, it's revealed the reader didn't see him because he was crushed by a giant force gem.