These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
An Aesop: Given the style of the series, it might have been unintentional, but Harkinian's advice to Link in part 2 of Episode 12 regarding his problems with Mary-O provides the lesson that you have to stand up for yourself if you want to stop being picked on and it's much better to face one's problems in life head on rather than freaking out and running away.
Dude, Not Funny!: The jokes about Link being mentally ill are going to strike a few sour notes among viewers.
Some of Mary-O's bullying might hit too close to home for those who were bullied in school.
An in-universe example seems to be Mario Head, who scares the crap out of Harkinian when he shows up in Episode 8.
In Episode 10, Ganon tries to kill Zelda. No jokes, no silly mannerisms, he just straight up tries to kill Zelda.
"Enough talk, MURDER TIME!"
Mary-O and Luigi's bullying of Link during class in part 1 of Episode 12 is just petty Jerkassery. Their bullying of Link in part 2, however, is outright disturbing, probably because how realistic of a depiction it is.