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.
Starfleet in general, with its tendencies to act as a multiversal police force and army, can seem like an evil overlord's armed force, making sure that everyone obeys the whims of the Unicornicopian overlords.
The sequel adds Goldwin to it, an Expy of Jeff from Today's Special. Several episodes in My Brave Pony: Star Fleet Magic II (which plagiarize entire episodes of Today's Special) are made specifically to involve Goldwin, even when they add nothing to the overall plot whatsoever.
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 gets a lot of the basic facts about FiM wrong in the story. For starters, the author believes Rainbow Dash has magic (to be fair, pegasi have a latent magic in them that allows them to control the weather, but it's not the same as the unicorns' mystical powers) and doesn't know who Derpy Hooves is.
To be fair, 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 character with a handful of speaking parts. One could watch the whole show and never know why Derpy's such a huge Ensemble Darkhorse.
Designated Hero: The heroes are this to some extent. As described elsewhere on this page and even the main page, their practices and beliefs can be very questionable, if not outright horrible. About the only thing that could prevent them from entirely qualifying is the fact the main villains are often legitimately evil and not Designated Villains.
Designated Villain: May not exactly be an in-universe villain so much as merely an in-universe loser, but Ace Ray can still qualify.
Chapter five of My Brave Pony: Star Fleet Magic III teaches that anyone who doesn't like you should be arrested, sent to an insane asylum, and brainwashed.
Hilarious in Hindsight: Mykan always wanted to make a more action-oriented story than Friendship Is Magic, to no real avail. Come the season 4 finale, suddenly the show he hates gets an action sequence that blows any he could make out of the water (not like that's particularly hard). Irony at its finest.
Idiot Plot: In the seventh episode of My Brave Pony: Star Fleet Magic II, a robot attacks a dam. Nopony can figure out it's not a living being despite noticing it's made of metal and shoots Eye Beams until its wiring is exposed.
Moral Event Horizon: The Grand Ruler crosses it in My Brave Pony: Star Fleet Magic II, when he actually makes Twilight believe she is responsible for an entire family getting hurt, just so he can teach her that she should always follow his orders blindly.
Narm: Twilight's death is presumably supposed to be a Tear Jerker moment, and is built up to be tragic. So naturally, Lightning responds thusly.
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.
Aside from padding in-chapters, Mykan seems to have an obsession with writing 26 episodes per-season, which leads to many episodes where nothing advances the plot. The biggest offenders are in My Brave Pony: Star Fleet Magic II.
Painful Rhyme: Rhymey. There is a reason why he's the most hated character out of the lot.
Taken Up to Eleven in My Brave Pony: Star Fleet Magic II, where there is an entire chapter writen in rhymes. Ironically, it may be one of the better chapters in the entire story as it plagiarizes an episode of Arthur.
Sequelitis: The original story has four sequels and counting, one's a "movie" and another is based on My Little Pony Equestria Girls, and they don't get any better. Beats0me, a DeviantArt member who draws parody comics of MLU, noted that the beginning of the series is So Bad, It's Good, reminiscent of watching a corny old kids' action cartoon. However, the further it goes on, the more racism, sexism and other disturbing content start cropping up.
They Just Didn't Care: An admitted case. The author pretty much states that he doesn't care about the originality of the fic and doesn't bother with characterization.
In one story, Fluttershy almost dies due to severe appendicitis. Mykan was aware ponies don't have appendixes, but chose to do the plot anyway.
They Wasted a Perfectly Good Character: Cerise from My Brave Pony: Star Fleet Magic II is a major in Starfleet, can stand toe-to-toe with Lightning and can use the Uniforce. She is a one-shot character.
It may sound farfetched, but the relationship between Lightning and the Grand Ruler could have been quite an interesting plot arc in the hands of a better writer.
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 My Brave Pony: Star Fleet Magic II, 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.