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.
Unicornicopia: Paradise on Earth, or autocratic dystopia?
Titan: Complete Monster with no redeeming qualities at all, or a bitter old man who lost his mind because no one ever gave him a chance, leaving turning to the dark side as his only option?
Starfleet in general, with its tendencies to act as a multiversal policeforce and army, can seem like an evil overlord's armed force, making sure that everyone obeys the whims of the unicornicopian overlords.
One of the many Aesops given out by the Grand Ruler can be summed up as "There are different ways to solve problems."
Another one deals with how nightmares are frightening.
Cliché Storm: Let's see... The villain is an Obviously Evil wizard who lives in a dark castle in the dimension of darkness. His minions are a Terrible Trio consisting out of a shallow Vain Sorceress, a schemer, and a brute, none of whom possess any redeeming or positive qualities. On the other hoof, we have a realm of good where the unicorns live happily without any personal conflict between each other, are ruled by a wise king and protected by a group of Super Sentai/Magical Girl-inspired good guys, whose leader has a fairy sidekick, defeats monsters with Sailor Moon-based moves and has to learn to believe in himself.
Ironically, while the author is willing to shout at everyone who makes fun of his characters, he does not care for the majority of them at all, ignoring them completely if he thinks that they serve no purpose for him anymore outside of battle scenes.
Critical Research Failure: Mykan get the basic facts about FiM wrong in the story. The author believes Rainbow Dash has magic, doesn`t know who Derpy Hooves is, and has no knowledge about Luna`s new speech pattern.
It's actually perfectly understandable that he doesn't know about Derpy. She's the epitome of Ascended Fanon, and only appears in-show as a background pony with a handful of speaking parts. One could watch the whole show and never know why Derpy's so important to the fanbase.
Moral Event Horizon: Grand Ruler crosses it in the sequel, when he actually makes Twilight believe she is responsible for the death of an entire family, just so he can teach her that she should always follow his orders blindly.
Padding: The author outright admits to using this, as he believes he has to fill a word quota. More specifically, he believes that every chapter has to be an equivalent length to a half-hour TV episode, with no exceptions.
Amazingly, he complains in the author's notes of the third series about how long his fanfics are, and yet does nothing to fix this.
Painful Rhyme: Rhymey. There is a reason why he's the most hated character out of the lot.
Taken Up to Eleven in the sequel, where there is an entire chapter writen in rhymes. Ironically, it may be one of the better chapters in the entire story.
The entire concept of another world of ponies having their own adventures and learning valuable lessons about the important things in life while also fighting against a common enemy could have been made entertaining (it worked for My Little Pony with FiM) if the author would not depend so much on clichés.
What Do You Mean, It's for Kids?: The story preaches that things like love and tolerance are actually worthless and only brute force can lead to true happiness. Characters get Killed Off for Real in rather brutal ways for little kids, and there are certain sexual innuendos to be found in the entire story. Yet the author proclaims that the fanfiction is way better entertainment for kids than the actual show it rips off.
The best example for it may be a chapter of the sequel, in which Fluttershy is in the hospital to be operated on. A changeling slips in and tries to kill her by cutting her open and letting her bleed to death.