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.
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.
Complete Monster: Ganondorf, presented here as a selfish and sociopathic king, attacks Link when the latter is a child, poisons the Great Deku Tree, and is heavily implied to have killed Zelda's father. Ganondorf is also a horrific master, brainwashing his entire Gerudo tribe with Twinrova's aid. Some of his own monsters serve him unwillingly: Gohma was a harmless spider that he painfully mutated into the monster that killed the Deku Tree. Ganondorf would also turn Volvagia, a benevolent, sentient dragon and Link's friend, into a mindless beast that Link was forced to euthanize.
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.
Genius Bonus: Like in the Japanese version game, it's possible to understand the Minish before Link eats the Jabber Nut. All of their lines pre-Jabber Nut are written in Japanese but are phonetically backwards.
Woolseyism: In the original Japanese version of the story, Link refers to Ezlo as a turtle, referencing the Japanese folk tale of Urashima-taro. In the English version, Link calls him a leprechaun.
Phantom Hourglass - Akira Himekawa
Complete Monster: Bellum here is given sapience, yet still carries out his atrocities to fuel his sadistic appetite. The Arch-Enemy of the Ocean King, Bellum would drain his foe's life force to the point where he becomes a frail and weak old man, Oshu, as a result, and would still drain Oshu's remaining life force, slowly killing him. Bellum would then use the Ocean King's temple to drain the life-force of the Ocean King's inhabitants, while constructing the Ghost Ship to find and lure countless more victims; including Linebeck's crew and Tetra, whom Bellum petrified. He would then possess Linebeck and force him to kill his friend, Link, before allowing Linebeck to commit suicide so he can consume his life force afterwards. Forced out of Linebeck's body, Bellum would drag the Ocean King down further depths of the sea in an attempt to kill him.