Creator's Pet: Eian is notably disliked, especially among those who read the original script, primarily for being a blatant self-insert of Joe_Cracker and making many jokes that either reference pop culture or are otherwise also unfitting to the tone the story attempts to have. Not helping with this is how he is also Impa's brother and he even manages to steal Ganon's Triforce of Power.
Both the original script (and by extension Part 3) have a plot point that involves the creation of the Master Sword, which requires using three keys named after the Golden Goddesses to unlock a chest containing the magic to transform Link's sword into it. The Master Sword would be given an official origin story years later with The Legend of Zelda: Skyward Sword, and its creation there also requires three items named after the goddesses (in this case, the Sacred Flames) to transform Link's sword into the legendary blade.
The second boss Link faces in the script is a giant frog that he defeats by throwing bombs into its mouth. The later-released Legend of Zelda: Twilight Princess would have the Deku Toad, a giant toad that is the miniboss of Lakebed Temple and is susceptible to Bombs and Bomb Arrows. Later down the line, The Legend of Zelda: Tears of the Kingdom would also introduce the Frox, a giant frog mini-boss that can also be stunned by throwing bombs into its mouth.
So Bad, It's Good: Done intentionally with the shorts to lampoon the poor quality of the script. The script they were based on is genuinely this.
Script
Narm: A lot of the original script, largely due the amount of spelling errors and dialogue. Special mention goes to a line that was replicated in the videos: "I cased over the moon..."
The dance sequence in Part 2 comes out of nowhere after Prince Facade talks about Tingle, and then everyone's dryhumping/dancing/slicing each other. Afterwards, it's like nothing ever happened. In the original script, the Triforce of Courage just speaks.
Zelda's face briefly turning into an even worsely-textured (and surprisingly pretty creepy) face in Episode 3.
Growing the Beard: The first short was just a short demo meant to confuse Joe_Cracker into thinking his movie was actually being made by DiC. The latter two are clearly meant to lampoon the script.
Take That, Scrappy!: The animators inserted non sequitur sequences of Joe_Cracker's Author Avatar Eian getting killed into the third short.
Tear Jerker: The trailer for Part 4 notably features a seemingly-lifeless Zelda laying on the floor of a volcano and Link trying to attack Ganon only to presumably be killed by him, as the next shot after the title shows the Master Sword shattering with the hero nowhere in sight. It's actually kind of hard to not feel some level of pity for Link and Zelda in the trailer.
Visual Effects of Awesome: Ganon's model and animation is actually professional in terms of quality, especially compared to the other characters. His model is very detailed-looking and his animation is very fluid and expressive.