History YMMV / MyBravePonyStarfleetMagic

** It is often speculated that [[spoiler:Twilight Sparkle]] was Raven's true target instead of Celestia and that Raven was working for Celesto the entire time. This is due to Celesto ordering everyone, including members of Starfleet, to not fight Raven despite her targeting ''his own wife'' with the excuse that her strength is unknown[[note]]Which is espically odd as Raven is an Equestrian, a species that the story claims is incapable of matching the strength of even the weakest Space Pony, let alone Starfleet's strongest and most experienced soldiers. Also, Starfleet almost never hesitate to fight other villains who are just as, if not more, dangerous than her, both before and after Season III[[/note]] and her plothole-riddled backstory[[labelnote:explanation]]As pointed out by Twilight in ''Fanfic/FallOfStarfleetRebirthOfFriendship'', “Let’s ignore that Ponyville didn’t even exist until ninety years ago and focus on the two important things. One is, why didn’t Celestia teleport to the bad guys who had stolen her jewels instead of flying. Actually, why was she even with the royal jewels anyway and what criminal would be stupid enough to attack in broad daylight and in the presence of the princess herself. Second, what guard would hear “please help me!” and think “Hmmmmm, she is trying to get in the way, oh well. I’ll just ignore her.” No guard would be so stupid as to do that! And then you just magically disappear, that quickly? What you didn’t stick around. Wait, one last question. If you are a unicorn, then you had telekinesis, if you had telekinesis, then why didn’t you just lift up the carriage with your magic and save your husband.”[[/labelnote]]. Then came ''VIII'', which revealed that Celesto is aware of everything that occurs in United Equestria which only added fuel to the fire. While Raven is strong enough to use the Uniforce, and Celesto at least makes sure he doesn't directly send anyone weaker than Raven to their deaths, he had trained as much as her and more, his Uniforce is supposed to be the best there is, and he could have stopped Raven himself (which even Mykan admits would be a close fight), which he didn't... despite risking his life to duel another equal of his, Pinsar.

* UnintentionalUncannyValley: The Unicornicopians are represented as pony heads on top of humanoid bodies, and later the Equestrians are forcibly converted into being the same thing. The result is completely unsettling, with some characters resembling colourful [[https://en.wikipedia.org/wiki/Tikbalang tikbalangs]]. Not helping is how obviously photoshopped the images are.

--->''No one had ever broken out from this asylum, and even If they had there was no way they could leave the planet. The warp portals that led out into Dimensional Space were inaccessible by all convicts. Any one of them who tried to enter only got tossed back out again.''[...] '' Poor Ace, he did not take being locked up very well, and continued to insist he wasn’t insane, only to be restrained and sedated by the medical staff.''

** [[VagueAge It's not known how old En Shi is]], though she is certainly old enough to join Stammadon's first campaign, but her harassing, obsessing over, kidnapping, and assaulting Swift Star, who's 16 at the time, can be pretty disturbing to read, [[WhatDoYouMeanItsForKids especially since it's meant for kids]].

** As demonstrated by entries on this page and his character entry on this very site, Swift Star is quite well liked, even among readers who dislike Starfleet. This is due to him being [[TokenGoodTeammate a genuinely heroic figure]], who ([[LawfulStupid in contrast to his superiors]]) [[ScrewTheRulesImDoingWhatsRight is willing to face evil despite orders]] and even try and redeem certain villians, despite Starfleet's views on redemption. Him being blamed for being kidnapped only makes readers take his side. He's also far more tolerant of those who dislike Starfleet, only taking issue with them when they break the law and not actively looking down on them. He even manages to influence Lightning Dawn to be a better pony, inspiring him to stand up to Celesto when he refuses to let them rescue Swift. So, in recursive stories like ''Fanfic/StormwolfAdventures'' his role expands further, with this story in particular still painting him as a genuine hero who ''intentionally'' changes Starfleet for the better.

** As demonstrated by entries on this page and his character entry on this very site, Swift Star is quite well liked, even among readers who dislike Starfleet. This is due to him being [[TokenGoodTeammate a genuinely heroic figure]], who ([[LawfulStupid in contrast to his superiors]]) [[ScrewTheRulesImDoingWhatsRight is willing to face evil despite orders]] and even try and redeem certain villians, despite Starfleet's views on redemption. Him being blamed for being kidnapped only makes readers take his side. He's also far more tolerant of those who dislike Starfleet, only taking issue with them when they break the law and not actively looking down on them. He even manages to influence Lightning Dawn to be a better pony, inspiring him to stand up to Celesto when he refuses to let them rescue Swift.

** Brass Bolt for speaking out against Starfleet's draconian nature. The author tries to take sympathy away from him by having him release a bunch of prisoners, but seeing how our DesignatedHero cast mistreat the prisoners, it actually makes him more likable.

** Kitty Snip, a one-shot villain from [[https://www.fimfiction.net/story/378005/24/my-brave-pony-starfleet-magic-season-vi/episode-23-the-ties-that-unbind-us the twenty-third episode of]] Season 6, left enough of an impact on Scipio Smith he decided to [[AscendedExtra include her]] in ''Fanfic/MyBravePonyStarfleetNemesis''.

** The Insectos in ''Starfleet Magic V''. Unlike most villains, the Insecto royals actually have a better family dynamic than any of the heroes, making them easier to sympathize with, especially as Pinsar actually says that he served Titan in part to keep his family safe. Additionally, they can easily be interpreted as {{Proud Warrior Race Guy}}s rather than AlwaysChaoticEvil, as the only evidence of them doing anything evil is [[UnreliableNarrator the word of Starfleet]], and the destruction of their own planet is too StupidEvil for some readers to buy. And Pinsar becomes more sympathetic when he charges into battle because of ''speculation'' that his daughter is in peril.

* SignatureScene: [[spoiler:Twilight Sparkle's death in season 3]]. It's so infamous that even the author himself likes to talk about it.

** In IX, Artie and human!Sunset Shimmer just... develop feelings at the very beginning of the season. It's also blatantly obvious that this only exists to parallel human!Artie and Sunset Shimmer's relationship, which is another example of this trope.

** Twilight Sparkle is another character that Mykan hates for [[https://www.fimfiction.net/blog/690404/im-true-to-myself-3-rant-why-i-hate-twilight-sparkle utterly ridiculous reasons]]. Shortly after Equestria is introduced in the rewrite, she loses her wings (though at least she gets them back offscreen), the MLP cast as a whole TookALevelInDumbass, she's called out for not following the Grand Ruler's orders no matter what, and of course [[spoiler:she is murdered, which Starfleet and Celestia [[UsefulNotes/VictimBlaming blame her for]] and the latter takes up her mantle as the Element of Magic]]. This even extends to ''Starfleet Humans''; the human Twilight Sparkle gets yelled at by Lightning regularly over petty things.

** Despite suffering from [[TookALevelInDumbass the same fate as her fellow Equestrians]], Twilight Sparkle herself is this for at least being among the closest to her canon self, as well as gaining pity points from viewers who rightfully believe [[ButtMonkey she's treated horribly by the Space Ponies]]. [[spoiler:Her death at the hands of Raven has also sparked several more accusations of Starfleet being unlikable, due to them [[UsefulNotes/VictimBlaming blaming her for her own death]] because she [[SugarWiki/MomentOfAwesome disobeyed Starfleet to protect those she cares about]]]]. After all that's happened, it's hard not to see her as TheWoobie. Cadance is also this, for the same reasons (just replace [[spoiler:death]] with [[spoiler:having a miscarriage and her and her husband being rendered infertile for life]], and you're golden).

** [[spoiler:[[UsefulNotes/VictimBlaming Celestia blaming Twilight for her own death]] gets even worse as ''[[Recap/MyLittlePonyFriendshipIsMagicS7E1CelestialAdvice Celestial Advice]]'' shows that [[LikeADaughterToMe Celestia pretty much acted like a second mother to her]]. By having Celestia act like this, she's not just blaming her student; she's blaming a pony she'd grown attached to since youth]].

* ItWasHisSled: [[spoiler:Twilight Sparkle is killed in ''III'', and Starfleet and Celestia [[UsefulNotes/VictimBlaming blame her for her own death]]]].

** Mykan's hatred of [[spoiler:Twilight Sparkle, her death, and the subsequent UsefulNotes/VictimBlaming]] have since become well-known despite all the spoiler tags surrounding it. [[Fanfic/FallOfStarfleetRebirthOfFriendship Two]] deconstructions [[Fanfic/MyBravePonyStarfleetNemesis occur]] afterwards.

** Despite the controversy surrounding it, [[spoiler:the idea of teaching about the death of a loved one could have been a good idea had Mykan just focused on meaningful character interactions and development instead of UsefulNotes/VictimBlaming and his own hatred for the pony in question, Twilight Sparkle]].

* EvilIsSexy:
** [[spoiler:Fratello]] is rather handsome, with a {{Bishonen}}-esque design. Downplayed, in that [[spoiler:this is what he looked like before his FaceHeelTurn]].
** En Shi is also mentioned to be very attractive, despite being one of the most vile characters in the whole series.

* CanonDefilement: While the fic itself is often loathed for making the cast of ''[[WesternAnimation/MyLittlePonyFriendshipIsMagic Friendship is Magic]]'' less competent to make Starfleet look superior, Celestia in particular is given the worst of it when she [[spoiler:[[UsefulNotes/VictimBlaming blames Twilight Sparkle, her own student, for getting killed instead of blaming Raven for killing her]], and pretty much acts as a ReplacementGoldfish for the Element of Magic, even though Celestia would never pull this kind of thing in canon. [[DesignatedHero And she (along with Starfleet) is supposed to be in the right for thinking this]]]].

** In Chapter 20 of the original fanfic, it's revealed that Serpent Tyrant's motive for collecting the Rainbow Stones is to undo the speciecide his son Titan had caused. Other than being told the supposed Dimension of Darkness's denizens are evil, there are no indications of them committing great atrocities, and the readers only see things from a certain point of view — [[DesignatedHero The Unicornicopians]]. It's also not hard to see him as a WellIntentionedExtremist.

* SoBadItsGood: For some, the original fanfic feels as though it's a cheesy yet entertaining action-filled animated kids' show that would've been right at home in the '80s and '90s. This eventually falls by the wayside with the sequels.

* SoBadItsGood: For some. The sequels are a much different case as shown by the {{Sequelitis}} entry.

** [[ArcVillainess Windy Bag]] from ''VI'' is an JustForFun/{{egregious}} case; her EvilPlan boils down to kicking Starfleet off of Equestria. Considering Starfleet's DesignatedHero status and treatment of the Equestrian population, it's not hard to see her as a WellIntentionedExtremist at worst. It helps she also has a vendetta against a blatant AuthorAvatar, and a particularly jerkish one at that. Similarly, the Idiots in ''X'' also want Starfleet and only Starfleet out of Equestria. They aren't like [[AbusiveMom Windy Bag]], and care not to hurt those who don't support Starfleet. As a result, they end up likable.

** In Chapter 20 of the original fanfic, it's revealed that Serpent Tyrant's motive for collecting the Rainbow Stones is to undo the speciecide his son Titan had caused. Other than being told the supposed Dimension of Darkness's denizens are evil, there are no indications of them committing great atrocities, and the readers only see things from a certain point of view - [[DesignatedHero The Unicornicopians]]. It's also not hard to see him as a WellIntentionedExtremist.

** In an actually decent twist, in chapter 20 of the original badfic, we find out that Serpent Tyrant's motive for collecting the Rainbow Stones is to undo the speciecide his son Titan had caused. Other than being told the supposed Dimension of Darkness's denizens are evil, there are no indications of them committing great atrocities and we are only seeing things from a certain point of view - [[DesignatedHero The Unicornicopians]]. It's also not hard to see him as a WellIntentionedExtremist.