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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.
Alas, Poor Scrappy: The Cosmic Retcon that the G3.5 world was put through, seen from Pinkie's POV. Despite all the hate that particular gen, most readers have admitted feeling sad for their fate. This was pretty much the author's intent.
Invoked by Word of God with Loneliness. Her backstory was intentionally left vague as to promote this. Did she really love Trixie? Or was she just using a pretense of love to manipulate her? Is she just a creation of Trixie's twisted psyche or an evil entity that came from somewhere else?
Another one is provided by "AJ's Dream". She may be Trixie's Nightmare that was trying to come to the surface.
Luna's punishment of Fluttershy has been seen as warranted, a Moral Event Horizon, or even as too light by different groups of fans (and ponies, In-Universe). Likewise, whether or not Fluttershy has earned redemption for what she did or not is this, also both In-Universe and out. Even Fluttershy herself isn't sure, but she says she will always regret what she did and resolves to become a better pony from the experience.
Turns out that Fluttershy's punishment was largely Luna's reaction to Princess Gaia trying to take Pipsqueak from her, and seemed more about vengeance than justice. This over-protectiveness of Pip figures prominently in Luna's nightmare and develops her character during her side-story.
Celestia calls out Luna for mind raping Fluttershy, only to turn around and do the exact same thing when she and the Flutters are alone. While Celestia actively comforts Fluttershy afterwards, it's left up to the audience as to the Hypocrisy of her actions.
Some have interpreted Celestia and Luna as out of touch hypocrites who do not truly practice mercy and friendship, and that Celestia actually does have a habit of punishing people too severely. Of course, on the other hoof, there could be many justifiable reasons for it.
This trope is essentially invoked by the author whenever he gets the chance. Often a character's motivations, personality, and other traits are not spell out for the reader and interpretations in the comment are really approved or disproved by Word of God. This also boils down to whether certain actions (such as Celestia and Luna's actions above or the results of Princess Gaia/Nightmare Whisper's actions). Where they too harsh? Easily Forgiven? Bad people? The author rarely knows themselves and leaves it to the audience to decide for themselves.
This is here on the YMMV page for this very reason, the same scene can be seen in very different ways which ironically mimics the entire idea of having one story being told through various perspectives.
This Trope by definition is used for many of the "background" and "minor" characters as they're given a lot more to work with compared with their canonical portrayals. For example, Twinkleshine, the first background pony to speak in the show ever is re-imagined as Cadence's head of personal appearance, Octavia is given a relation to Pinkie Pie and has a special talent in rhythm, Minuette is actually The Master in pony form, or how the famous Blueblood is a Lonely Rich Kid who has a special talent in navigation and guidance.
Arc Fatigue: AlexWarlorn and some readers felt that Columbia in the Shining Armor arc went on too long (for example Makarov overstayed his welcome some time before the final battle with him). The Arc's author concedes maybe it could have been written faster, but probably not much shorter. Contrast with...
The sheer size of both the Wedding Arc and the Dark World Arc has been known to put more than a few readers off. There's a small but Vocal Minority within the fandom that considers large chunks of both arcs to be little more than filler.
Archive Panic: The fanfic is huge. The Canon story is already nearly 200 chapters long, and that's not even counting the "optional canon" side stories that get incorporated from time to time. As the producer of the audio adaptation said, it's long enough to make a sizable TV Series.
The Pantheon in general and Amicitia's giving various Dark Fics their happy ending. Some like the varied nature of the Pantheon, others feel they've become a Plot Tumor, and while people enjoy the latter, others thought it was a Take That that makes Amicitia too perfect for being capable of it.
The Land of Cats in the Shining Armor arc. Added without the knowledge or consent of the main author of the arc, noted by readers as being wildly out of sync and tone with the rest of the arc,had a number of plotholes, and is still opposed by the arc's main author. The defense that it was intended as a deliberate Cloudcuckooland largely fails to hold water against the problems contained within the chapter or caused by it - and the mistakes the chapter represents have done nothing but add to the Troubled Production.
The creator feud between Alexwarlorn and LZ. Some people think LZ was in the wrong, some thing Alex was in the wrong, and some people thing both are in the wrong or the both have legitimate complaints and points. Still others think both are just being too stubborn to let go of a grudge and just need to go their separate ways instead of fighting over something that's said and done and just let the past be in the past. Thankfully, Alexwarlorn and LZ ultimately came to a truce and their feud eventually ended.
Makarov himself. As noted below, some people found the arc's tendency to treat him as both completely ridiculous yet still a serious threat at the same time to be a bit jarring, whereas others thought that this disconnect made him that much more terrifying.
Queen Chrysalis seems to be this. She's either a scary, competent, dangerous villain or a Creator's Pet and Villain Sue. She's eventually revealed to be a Peggy Sue who managed to get a glimpse of the Heart World while Makarov had rendered her Ret Gone, thanks to being a part of Cadence, allowing her to compensate for the mistakes that version of her made.
The Wedding arc as a whole, really. Even the people that like the arc admit that certain parts of it could be handled better. Much like the actual Wedding Arc, funnily enough.
The Funetik Aksent employed with Apple Family members has served as a rather mild version of this. Some readers are okay with it, but others find it irritating - It is even claimed on the Pony POV Series page that the thick accents were a factor in Equestria Daily rejecting the fic for publication. It must also be noted it seems to have intensified in later chapters.
Better Than Canon: The fic gives this treatment to the entire G3 world. G3 is hated by a vast majority of fans, Gen 3.5 even more so. This fic successfully makes them into complex characters the audience can feel for. While the Alas, Poor Scrappy moment would be sad in its own right, the fact this was done first makes it downright devastating.
Word of God refers to Discord as an "egotistical, sadistic hedonist". That probably tells you a good bit of how monstrous this guy is.
It doesn't help that Discord's Mind Rape is actually described almost as if it's real rape, including one of the Wonderbolts stating she feels "violated" by what he did to her. And Discord does this for fun!
As bad as he is in the main timeline, he is even worse in the Bad Future Epilogue timeline, reviving the dead to feed on the living, having ponies mass executed for using magic, and letting Angry Pie and Fluttercruel go out and kill anypony they want, are pretty much the least to worry about. Probably the worst things are what he did to Derpy (turn her daughter Dinky into a muffin, and put a curse on her so that in order to turn her back to normal, Derpy would have to do a bunch of laps around his castle, while being attacked by hungry birds who wanted to eat Dinky, even after a thousand years of doing laps around the castle, she still had eight quadrillion left, and then she would have to repeat the process for her other daughter, Sparkler) and Fluttershy (trap her in her own body, and doom her to spend eternity being tortured by Fluttercruel, and being forced to watch all of her atrocities).
In Applejack's reharmonization chapter, we see several bad things he did to ponies, like turning Silver Spoon into tin foil, putting her eyes on her glasses, and making her father try to behead her, he also turns Blueblood into an ice sculpture of a mare and sends a stallion made of solar flames after her to rape her to death.
To sum up, as opposed to the more canonical view of him being a more malicious Equestrian Loki, this universe has him portrayed as a more whimsical Equestrian Satan. In fact, the actual Equestrian Satan was his Evil Mentor!
Reharmonised Angry Pie. Unlike the Dark world Angry Pie, this version has no redeeming qualities. She goes on a rampage killing all of Pinkamena's friends, and tries to kill and absorb the other Pinkies into her body so she can take over and become the true Pinkie. After taking over, she plans to kill all of Pinkie's friends in the real world. There is a strong implication that she actually likes killing, in fact, the audio adaptation even gives her a Slasher Smile.
She gleefully uses images of Trixie's own mother to Mind Rape her into catatonia, and tries to outright murder her and Twilight several times.
While Loneliness seems to love Trixie, Word of God intentionally left it vague as to if it was genuine or if she's like the Other Mother and just manipulating her cruelly to get what she wants.
Grogar is implied to be one as well, being compared to Darkseid by Word of God as well as that ponies had trouble deciding which one was worse when he and Discord fought one another. Word of God even says that had he won, his rule would have been every bit as bad as Discord's. We finaly get to see him in action in the Seven Dreams/Nightmares timeline, and he more than lives up to all the build up, he uses the rainbow fragment to move his base to earth, and removes his weakness to the belle. In his fight against Patch, Grogar gives her several third degree burns and a permanent limp that she keeps for the rest of her life. Grogar is shown to be incredibly cruel, and unlike Discord, he is played completely seriously.
The Pegasus Despot from Patch's chapter of Seven Dreams/Nightmares, who uses the Blue Shard of the Rainbow of Light (Laughter) to rule a city as an Evil Overlord. But that's not what makes him this. He uses the shard to brainwash mares, including Patch, into allowing him to repeatedly rape them. Some of them apparently rejected him before (given he was a fat nerd, it's not hard to see why), but some were simply innocent ponies who'd done nothing but caught his eyes. His Karmic Death was very satisfying.
The Valeyard. We only get glimpses of him for most of Dark World, but then he gets some focus when the Elements of Harmony storm the castle, and we see just how much of a monster he really is. He repeatedly killed the Master just for fun, and willingly and gleefully helps Discord with all his evil actions, while planning to one day steal his power and take over the universe, all to feed his god complex. What's worse is that, while even Discord has his care for Fluttercruel as a (somewhat) redeeming factor, the only joy the Valeyard gets out of his memories of his loved ones is remembering the times when they screamed and suffered. In his fight with the heroes, he tries to make Twilight evil again, reveals that he is NOT discorded, mocks Derpy for her plight, and uses several other cheap shots and dirty tricks. Aside from fighting dirty, he also uses Cold-Blooded Torture on the heroes at several points, with probably the worst moment being when he uses sonic screwdrivers on them. Fitting, as the Valeyard was stated in the series itself to be the personification of all the Doctor's evil and negative qualities.
The Nameless Passenger is quickly starting to become one as well, what with rooting Twilight on during her brutal No-Holds-Barred Beatdown of Angry Pie and trying to get Twilight to murder a completely innocent sea pony in cold blood just For the Evulz. It has even been said by Shady that The Nameless Passenger is WORSE than Discord (and so far, everyone seems to agree, including Discord himself). To top it all off, she plans to erase the Dark world timeline from existence and kill all the inhabitants in the process. She later reveals that she's done this enough times to add up to several hundred million years and doesn't feel one ounce of guilt for it.
Makarov from the Shining Armor Arc, goes around eating others just to increase his power. He also trapped four other ponies in an And I Must Scream fate, killed his parents, launches an attack on a village to try and kill everyone, and causes a war leading to the deaths of thousands if not millions of innocents. The reason? To make himself look like a hero.
Screwball/Golden Tiara, who breaks out from the asylum by being too crazy and Bad Ass to be stopped by obstacles like hoof-cuffs, numerous security staff, reinforced doors, electric fences, or a cockatrice attack. The next we see of her, she's stealthed her way to Canterlot, at least partially by relying on a drainage system, which she fit through by dislocating her own bones, which is also how she managed to escape the asylum. Did we mention she can dislocate and re-set her bones? Because she can, and she refuses to let a little thing like pain that would knock a normal/sane pony unconscious stop her from saving her daughter.
Apple Pie. What else describes somepony who manages to Logic Bomb an army of zombies with what she thought was just an amusing observation? She is related to Pinkie Pie after all.
Her power as the Element of Laughter? Weaponized Logic Bombs!
Trixie and Chrysalis also fall into this category.
Doing It for the Art: Writing such an extended story and continuing to do so despite numerous production issues gets Alex this trope by default.
Ending Fatigue: With something of an overlap to the Arc Fatigue and Archive Panic examples above, the sheer size of the final portions of the story compared to other arcs alone may cause this to readers not put off by either of the two aforementioned potential stumbling blocks. Dark World and the Wedding are also notable for how many twists that throw into a whole new strand emerge, with many chances to end being nothing more than twists that just lead to even more of the same. Accordingly, if one actually does not mind those two parts and their Serial Escalation the slower pace of the Shining Armor arc may be a turn-off.
Ensemble Darkhorse: Havoc, Pandora, Strife, Destruction, and D___t. It must run in the family.
Lemon Hearts became this after just her first scene, due to that scene being extremely Badass.
Judging by reader reactions, Running Gag actually seems to be the most popular member of Misfit Actual.
Esoteric Happy Ending: Some consider the Princess Gaia arc to be this, as not only does Fluttershy not receive true punishment for putting literally millions of lives at risk over what was essentially a temper tantrum, but she even gets an entire holiday in her honor. Also, several people have noted how odd it is that the ponies of Equestria still majority consider the Mane Six heroes despite the Gaia arc showing them just how dangerous and uncontrollable the Elements can be. The author actually addressed the last one in "Under the Stars" to clear it up by detailing that every last Paradise Pony and everypony who used one of the Shards after the G2 apocalypse, as well as Patch, fit the profile for a Bearer, but none of them went Nightmare, and explaining Fluttershy doing it was due to the mental trauma caused by Discord and her being forced to see the cruel side of nature before she was ready (and each Nightmare shown in the truth were also the result of severe mental trauma that simply doesn't happen every day), meaning the Elements aren't so much dangerous as have an incredibly slim chance of allowing their wielders to become Nightmares (a ratio of 1 Nightmare in several hundred if not thousand Bearers, made even rarer by fewer ponies now having them).
It is also worth mentioning that a lot of ponies felt better after the effect of Gaia's fog compared to their own former traumata from Discord.
Fan-Disliked Explanation: Alexwarlorn noticeably tries hard to avoid this trope. There are certain things he simply doesn't want explained because it'd take away from their mystery or impact. He often gives multiple possible explanations for the audience when asked as well, even saying there could be others, as he feels some things should simply be left up to audience interpretation. This is best shown with Loneliness, who, despite being the first Big Bad, has never had her origins or what she actually was explained concretely. In fact, as the story progresses, more possible explanations have popped up for what she was. Word of God says this is entirely intentional.
This is also why he has avoided revealing just why Scootaloo's parents did what they did, because he fears that any explanation he comes up with will disappoint readers who had their own theories. It turns out that one of her parents was a renegade Changeling, and they had to flee to avoid agents of theHive, and have been searching for her.
Another moment that ties into the same discovery: in "Links," shortly before Pinkie Pie escapes from Princess Gaia's Lotus-Eater Machine, she says she had simply assumed that "reality had been rewritten again and we had moved onto generation five of the franchise." It's just Pinkie being Pinkie, right?…Until later, when we learn that she had witnessed the Cosmic Retcon that gave birth to G4 from G3.5's ashes firsthand.
Several funny moments regarding Discord in Dark World become this when its revealed Nightmare Paradox was responsible. Of note is when Discord stared at a TV test pattern for several centuries because Paradox rendered him catatonic making him witness his defeat and his daughter's death at the same time several hundred times.
In the first chapter of the Shining Armor arc, there's an amusing Running Gag that nopony seems to recognize Shining without his armor on. Then we find out why in part 2 of chapter 19...
Genius Bonus: You're going to need a cheat sheet when you get deep into the G3-G4 Generation Transition POV, as the level of Mind Screw is up there with Primer in the amount of things you need to hold onto at any given time.
Melody's given six minutes for her concert in her dying dream. It takes six minutes for the brain to die once your heart stops.
The unidentified material used to start the fires in Zebrawa included "iron, aluminum, sulfur, and evidence of some sort of barium compound", baffling the ponies who have no idea what it was. Military variants of Thermite, called Thermate, often include these substances. They're notable for burning at even higher temperatures than regular Thermite, making them even more useful at destroying things.
If you read this, then Sweetie Belle's strained delivery of "I like her... mane..." takes on a whole new meaning. She'd been turned into a living doll that kept swapping around its limbs by Discord. After that, she was scared of her own doll collection.
In the "Fluttercruel - Black Pearl" chapter, Fluttercruel asks Fluttershy if she'd like to make Rainbow Dash like an infant again, Fluttershy is horrified by the idea. Next chapter, Fluttershy goes Superpowered Evil Side and turns into Princess Gaia, who refers to everyone she's brainwashed as "her foals" and treats them like a mother caring for her children.
Onyx has Fantastic Racism towards the other two races of pony. "Hearth's Warming Eve" gave a valid explanation for why he might.
Pinkie's line "and that's how Equestria was made" from "Cutie Mark Chronicles". She does know, and its extremely tragic.
Makarov's endgame involves using chemical gas weapons to perform genocide on the Dragons. The chapter was actually planned and written before Syria launched a real life chemical gas attack.
Word of God compared Nightmare Eclipse to Homura, only in a darker, more evil sense...then the movie happened and the comparison became stronger, but Homura became more like Eclipse.
Shining Armor asks the Interviewers after he's killed the Blank Wolf if this will just allow more insertions like Makarov to infect the world, and they tell him not to worry about it. With Discord's final plan hinging on the wolf not being around, perhaps they should have been a little bit worried...
The fact King Sombra's reign over the Crystal Ponies wasn't just shrugged off and left deep, lasting trauma echos back to one the Pony POV Series was made in the first place.
"One Bad Apple" touched on the fact even bullies can be complex characters and have real reasons why they do things, one of the things the author was trying to accomplish with Diamond Tiara and Silver Spoon in this series.
Rainbow Dash takes Scootaloo under her wing ("Scootalove") rather early in the Pony POV series. Guess what happens in "Sleepless in Ponyville"?
While the end effect was the opposite of what happens in Pony POV (her personality gets more exaggerated instead of reversed), Trixie gets corrupted by an outside power in "Magic Duel" and ultimately becomes a better pony when cured.
Epilogue!Discord's favorite pony being Fluttershy, which "Keep Calm and Flutter On" rendered canon. Then Dark World!Discord was heavily implied to have seen the error of his ways, just like Canon!Discord did. Keep in mind Dark World was actually all planned and written before the episode was even revealed, even though the chapter was posted afterwards due to editing and Alex has refused to watch the season or see any spoilers for it until the fic is finished.
The Nameless Passenger was revealed to be Nightmare!Twilight. Canon!Twilight becomes an Alicorn in the Season Finale. The episode aired the next day.
It seems, in general, Season 3 is touching on quite a lot of the themes of this fanfic. Particularly hilarious because at the time these scenes were written, the author had not seen any of Season 3 and was actively avoiding spoilers.
The My Little Pony: Friendship Is Magic (IDW) Comic book had Rarity become a Nightmare as the Big Bad of the second arc. The villains of the story arc of the fic running along side it are Nightmares of all of the mane six except for Rarity, who was replaced by Spike. Even more ironically, Rarity is presently the only member of the mane six who's Nightmare hasn't been seen in any form.
The climax of Equestria Girls makes a good bit more sense in this verse than in canon since the physical Elements aren't needed to use the Elements and Sunset Shimmer's demon form could easily have been her Nightmare assuming she's a potential Element of Magic like Twilight and Trixie. Equestria Girls wasn't even thought of when that aspect of the series was introduced.
Trixie's Reharmonization Chapter begins with her talking about how long her Fan had been waiting for this. It took more than a Year till the Audioadaptation of that Chapter was released.
The Wedding Arc deals with, among other things, a conspiracy in the Royal Guard, with changelings infiltrating it and several pony cities, to the point where it's difficult to figure out who to trust.Sound familiar? (Even better, the author wrote the entire arc in advance a few months before the film came out).
The "Reflections" Arc of the comic confirms that, besides the "Equestria Girls" universe, there's an entire multiverse in canon.
During Dark World, Rainbow Dash gets a Super Mode called Ender Dash relating to her Element of Chaos. In the season 4 finale, the mane six get Super Modes based on their Elements.
HSQ: Dark World 24. I mean, Good Gravy! What a penultimate boss fight!
It would make an awesome final boss in any videogame and then things get even more epic with the real final boss.
I Am Not Shazam: Pandora stated she didn't want to talk about ____ or "Ruin" and many readers believed ____ was named Ruin, when she was actually talking about Destruction.
Iron Woobie: The Dark World heroes, both the redeemed Mane 6 and the Sixth Rangers. Given they live in a Bad Future, they're clearly hurting, but they don't let that stop them. Even Apple Pie shows she's suffered a great deal of loss and pain, but remains a hope filled optimist.
Fluttercruel. Yes, she's a Jerkass, but the way she described Fluttershy coming back into control and her being crushed up inside her and what it feels like for her to be the one whose stuck inside makes it nearly impossible not to feel sorry for her. The poor girl doesn't even consider herself alive, just a copy of Fluttershy…
Diamond Tiara is the poster filly of this trope…just as much of a bitch as her canon counterpart, yet it's hard not to feel bad for with her relationship with her mother.
Filthy Rich/Onyx Tiara. Think about it. If you were aware of how Pegasi and Unicorns once used your sun-species as effective slave labor, and how no one else of your sub species seems to care and in fact have friendships with them despite all that you and your kin endured because of them, wouldn't you be a little bitter?
Lawful Evil: Grogar is referred to as such in-universe. His goal was essentially the antithesis of Discord's, a world of absolute order run like a machine.
Like You Would Really Do It: Inverted. Many readers thought Traitor Dash was too far gone and would have to die, and were pleasantly surprised when the author managed to successfully redeem her.
Dark World 31 had Nightmare Paradox supposedly let loose a World-Wrecking Wave that kills everyone but Twilight and destroys all life on the world before making Twilight become her. Not only had Word of God already outright said Dark World would have a happy ending, there were still several chapters left and Fluttercruel was the Element of Kindness, something that wasn't possible in the present loop. Ironically, this actually managed to convince some people Dark World had a Downer Ending.
Even better (or at least hilariously) The event that lead the two factions to war, was the three ponies awakening the power of friendship. If the two sides going to war was something Discord engineered, then that means HE was the one responsible for the Magic of Friendship!!
Magnum Opus: Because seriously. If you devote over a year of your life to writing one story, and with the help of your team create a fic that's already over 90 chapters long, dripping with intrigue and interesting concepts, heartwrenching, awesome, heartwarming and even coming up with explanations for things never addressed in show while creating a compelling alternate universe, you better believe this trope counts. Of course, don't tell the author, or they might freak out over the expectation.
Marey-Sue: Invoked in universe by Pinkie Pie when considering how to "fix reality." She comments on how now that she's Sane and can still go Breaking the Fourth Wall with her antics, perhaps she's become a Game Breaker and too perfect. Though if you really think about it, the only way Pinkie could be considered Mary Sue material is how you view her Crazy Awesome yet Wise Beyond Her Years ways. She still has a personality of cheerful yet deep ways. She still gets hurt in fights and isn't the one to finish the job. She still makes silly decisions, and she isn't a Spotlight-Stealing Squad. (thankfully, the author's variety of chapters focusing on all the characters keeps that in check handily). She even has a bit of a breakdown trying to keep her universe connected to the Heart World.
A real Mary Sue later on appears as the main villain for Shining to fight.
Moral Event Horizon: "Origins", being a prequel explaining Discord's Start of Darkness, gives several equally horrific options for Discord, but thus far, the most obvious is rubbing it in Celestia's face how her actions lead to the Draconequi and Alicorn War and stated he gladly takes the credit for his own role in it and enjoys the result. Made even worse is Word of God has heavily implied that Discord did this entirely to twist the knife of Celestia's guilt for his own enjoyment.
And then there's eating his own brother and father (well, his avatar, but still), and feeling absolutely no remorse for it. In-Universe, the Paradise Estate ponies decide he's crossed this after his genocide of the Sea Ponies and Flutterponies.
Forcing Diamond Tiara to relive the moment when her mother went insane and tried to strangle her to death, a memory she repressed due to just how painful it was. He then rubs salt in the wound by telling her that it was all her fault her mother went insane in the first place! Just when you thought he was out of lines to cross!
If you started with Reharmonization, one of his MEH's is revealed in Applejack's vision, where we see what he did to various supporting and background ponies. Every Discording shown is absolutely sadistic, but the worst of all is what he did to Trixie.
The other is what he did when Dashie arrived in Cloudsdale.
While the previous ones, while horrific, were no less than his redeemable alternate selves, Discord's master plan definitely crosses this line: perform a Rewriting Reality spell to twist the world into a grim darkCrapsack World, and make it so it's always been that way. The worst part? He corrupts children into helping him (namely Diamond Tiara, Alula, and Tootsie).
The Valeyard in Dark World either crossed it roughly five hundred years ago with what he did to the Master (repeating what Discord did to him, only unlike Discord, Word of God has stated the Valeyard did it just to kill him over and over and over again.) or by using Sparkler (actually a fake) as a hostage to lure the group into his trap by threatening to kill her.
If he didn't cross it then, he most certainly crossed it with his absolutely sickening treatment of Derpy the following chapter or his horrific methods of trying to kill the group. Then there's the reveal that he did all of this without Discord's taint.
Dark World!Fluttercruel revealing she spent about five hundred years torturing Fluttershy in a mental Torture CellarFor the Evulz. And when its revealed that Cadence saved Fluttershy's spirit, Fluttercruel calls her a thief and is mad her favorite 'toy' got 'stolen'. Made worse by the fact that she considers Fluttershy her mother and calls her such. Possibly subverted, considering she was genuinely so insane she believed she was showing her mother she loved her with the above, and ultimately realizes it was wrong.
If not there, she certainly crosses it by trying to convince Twilight to murder a completely innocent sea pony in cold blood even though, as the Benevolent Interloper points out, they don't need to do so to stop her from doing what the Passenger doesn't want her doing.
Turns out she crossed it a long, long time ago by coming up with a plan to punish Discord for eternity that involves repeatedly erasing the Dark World timeline from existence to trap him in a "Groundhog Day" Loop for eternity, erasing all its inhabitants as well.
General-Admiral Makarov/The Shadow Of Chernobull crossed this either by by taking four innocent ponies based solely on the irony of their names to convert into his Alicorn Cyborg Co-Dragons (which condemned them to an And I Must Scream fate), or by slaughtering an entire innocent village so as to Leave No Witnesses. This is also the point where he's considered by the characters In-Universeas having crossed this line.
Queen Chrysalis did plenty of horrible things, but the point were she definitely crosses this is with the reveal of her real endgame: use a rune to rip the emotions out of every creature in Equestria and absorb them to become a being even stronger than Discord. Let us reiterate, Chrysalis is such a monster she's willing to reduce an entire country to Empty Shells for power simply because she wants power (instead of the more sympathetic motive of being for her Changelings: the Changelings don't even know this is what she's really up to!).
If not then, her putting an illusion spell on Twilight so she'd see and hear Cadence as Chrysalis if she was freed from the primary mind control and kill her in her rage. It's implied by her dialog her main reason was simply sadism and to try and one up Discord.
Narm: Some readers felt that the Shining Armor arc's attempts to treat Makarov as completely ridiculous but still a serious threat to be a bit jarring at points.
Not anymore. She's one of Nightmare Paradox's Psycho Rangers.
Paranoia Fuel: The Gaia Festival. Imagine living in a world where you made a mistake, and because of that mistake hundreds, if not thousands of vengeful, murderous ponies are lurking in the shadows, hellbent on murdering you horribly, and you have no way of knowing if your so-called "friends" are truly friends, or one of those vengeful ponies. That is the world Flutterhy now finds herself in.
Player Punch: Sunset and Ranger's deaths are this. Especially due to the suddenness of it.
At least attempted in the Wedding Arc a few times, but sadly more often than not, more likely feeling like an Ass Pull at best, outright God Moding at worst.
Some people thought that these were pulled off fairly well- see Broken Base above.
Plot Hole: Some of the dreams in Shining Armor 18 are a bit... inconsistent with what has gone before, and to a degree that cannot be adequately explained or handwaved by Makarov's deletion.
The whole of SA 19's first part is a plot hole, though the second part (when Alex and LZ started directly collaborating to finish the arc together) manages to fix most of them.
Plot Tumor: The whole "Apocalypse of G3" arc and all the other cosmic sidestories spun off from it.
However, it doesn't really affect the main story line that much, outside of a few character's back-stories and setting up the Origins Arc.
One might also consider the Princess Gaia arc and everything after it this. Before that whole lot was launched it looked like Diamond Tiara's actions had freed Discord and it was time for Round 2. And now there's yet another segue in the form of the Dark World storyline.
It becomes less this when one thinks of each story arc as a separate season (which is how they're presented on FIMfiction) with the overall story arc being Discord's third coming.
A more minor example is Ace from My Little Pony Tales, by having him refuse to leave Melody no matter what and generally be a good husband for his wife, having mellowed out from the Jerkass he was in canon.
Flash Sentry's appearance seems to fall into this trope, as he's given a more interesting personality and actually covers Twilight during her fight with Death Stalker while actually taking some bruises for his efforts. If nothing else readers find him interesting and his brief appearance imply some greater mystery to his character.
Rewatch Bonus: While there's still enough foreshadowing, reading the Dark World Arc again makes The Reveal that Rancor is the Sixth Ranger Traitor to Discord's team make more sense, as there are several bits of foreshadowing that are easy to miss the first time around.
Likewise The Reveal of Dark World!Discord being trapped in a "Groundhog Day" Loop by the Nameless Passenger also makes a lot of previous moments suddenly make sense especially Discord's habit of freezing up whenever he mentions something being repeated.
There are TONS of bits of foreshadowing scattered throughout the entire story that first-time readers might not pick up on at first, but then remember it when it finally pays off.
Celestia and Luna get this from fans, mainly due to their treatment of Fluttershy (which overlooks the fact she just tried to take over the country, brainwashed billions, and nearly killed billions of unborn children, and is now an Alicorn who needs to see the true gravity of her mistake in order to properly adapt to it) and Celestia's punishment of Nightmare Moon and Discord, despite being confirmed both the fic's Word of God and the show'sWord of God that she fully intended to redeem Luna but couldn't herself. Discord's is mainly due to Draco in Leather Pants. He has had a few Pet the Dog moments, and had a pretty screwed up childhood, but he's still backstabbed EVERYONE who tried to help him get better, committed two completely unprovoked genocides, one of which would make the NazisFinal Solution look tame by comparison, and generally been an utter Complete Monster who only cares about and gleefully admits to it. The fic itself avoids these tropes, it's some of the fans who don't.
Of course, on the subject of the fic avoiding it, well, YMMV...
Rule-Abiding Rebel: Sure, Anarchy might consider some things stupid or out of line, and his job is to incite rebellion, but he always does so due to his position.
Seasonal Rot: The Wedding Arc has poorer editing than previous chapters, has some potential pacing issues, is sometimes inconsistent with established events and even itself, expands the potential for Archive Panic and Ending Fatigue, and also risks Arc Fatigue with the sheer length. Even the people that like the arc think that certain parts could be handled better.
Squick: Golden Tiara (a.k.a. "Screwball") can squeeze through tight spaces with ease, like slipping through cell-bars or squeezing her way through drainage systems. How does she do this? Why, by voluntarily dislocating her own bones.
Golden Tiara: "Ya disconnect this bone connected to the hip bone, you disconnect this bone connected to the shoulder bone, you disconnect this bone connected to the neck bone, wait, better not touch that one on second thought. Fold myself up, if I try really hard I'm sure I could fit into a soup can. Really scared the hay out of an orderly one time, you'd think they'd never saw a mare hiding in a box half her size before! Took a while to get out, especially since he fainted on top of me."
Strife and Mortis have had kids together! To clarify Strife is draconequus (like Discord, and you all know what he looks like) and Mortis is part skeleton!
Strawman Has a Point: While it's clear she's taken it toofar, Nightmare Eclipse's desire to punish Discord is, given the severity of his crimes, at least an understandable one. Even the Mane Six seem to concede as much In-Universe, their problem is she's basically trapped everyone else in Hell with him.
Squick: The description of Queen Cocoon from Chrysalis' Origin Story. Chrysalis has good reason to be disgusted by her appearance.
Surprise Incest: A YMMV thanks to things being a bit complicated to say the least, but as Shining Armor was created from Amicitia, this means he is technically Cadence's brother as well.
They Really Can Act: The cast of the Audio Adaptation. Almost all of them are almost complete unknowns with almost no prior voice acting experience, they all deliver some amazingly convincing delivery. Absolutely selling the characters breakdowns and emotions. Special mention must go to Robot Butterfly (Who sadly had to leave) and Wollffeey. especially Wollffeey. Who's voice for Pinkie Pie is so spot on, you'd be forgiven for thinking they'd somehow managed to hire Andrea Liberman.
They Wasted a Perfectly Good Character: Rancor. She's just gained a power up by taking Destruction's power! What's she going to do with it? ABSOLUTELY NOTHING! Because she's probably never going to appear again!
In the author's defense, she was probably meant to be a one-shot character.
According to Word of God, this was an intentional and part of her character. She was meant to show up, throw EVERYONE'S plans into chaos, then leave. Hence the name she picks; Disruption. That and stealing Destruction's power was her plan, her use for it is simply to take up Destruction's job.
Uncanny Valley: Chrysalis's foalhood falls into this. Instead of being a straight up psychotic Creepy Child...she's a child first with the traits of a budding Sociopath already beginning to show themselves. In a strange way, it makes her more creepy than the former ever would have.
Unexpected Character: Who expected Moondancer to have a prominent role in the Wedding Arc? Or be brainwashed by Chrysalis early on.
Villain Sue: Makarov, and depending on who you ask, Chrysalis.
In-universe, Applejack learns what could have happened had she remained in Manehatten: Big Macintosh would have taken up the Element of Honesty and become part of the Mane 6, while Orangejack would have embraced different talents, had a different Cutie Mark, and eventually been Happily Married and started a family.
Also in universe, is Luna telling Fluttershy how, if she'd behaved a little differently, her paradise might have been closer to being achieved and she might have even come out OK from it. We even see an Alternate Universe where she took Applejack's suggestion of being honest with her followers, with their support allowing her to conquer the suffering she'd sealed away.
The entire G3 world. No matter what your opinion on that gen was, its hard not to feel sorry for them after what they're put through, especially after their fight to save their world ultimately .
Bon Bon's sister Moth probably qualifies too. She actually is a Changeling who honestly does love Lyra, Bon Bon, and the duo's adopted daughter, and hasn't harmed them, but showing genuine love for them is physically uncomfortable for her (basically, it's the changeling equivalent of vomiting) and events like Twilight's use of the Want It Need It Spell nearly kill her. Her reaction to the Spa Twins also implies she's to some degree terrified of other Changelings. Gets increased in the Wedding when her kind launch their invasion, making her terrified for her life. Not to mention that she gets beat up a lot after revealing herself to the heroes.
Rarity's reharmonization chapter reveals that she went through disturbingly realistic post-traumatic stress disorder after Twilight brought her back to normal. Poor thing.
Derpy, in both universes. Taken Up to Eleven in 'The Ultimate Foe', where the Valeyard takes great glee in pretty much tap dancing on every emotional scar she has.
Again in 'Crushed Pearl Necklace' when her daughter Sparkler has to be killed due to having been possessed by Cruelty.
Dark World!Rainbow Dash both before and AFTER her Heel-Face Turn. Before she's a conflicted, guilt-ridden Tragic Villain who hates herself for what she's done under Discord. Afterwards she finds some of her past actions coming back to bite her, finds out her childhood friend Fluttershy's been dead for five hundred years, and worst of all, finds out her best friend Pinkie Pie is dying of Rapid Aging. Then after the battle is over, Rainbow goes to hug Pinkie...only to go right through her; Pinkie Pie had died during the fight and been helping as a ghost ever since.
Stitches, an Earth Pony foal and one of Dark World!Fluttercruel's victims who had to watch her father die in a giant blender (It Makes Sense in Context) and mother and all but two of her siblings be slaughtered by Fluttercruel, all simply because they were healing ponies out of the goodness of their hearts. Then Fluttercruel gets her and puts her through a horrifying And I Must Scream fate while torturing her to death. It turns out that she is Fluttercruel's future self, implanted in the timeline into this family as an Ironic Hell for her crimes, and after realizing this goes into a Villainous BSOD when her memories return.
Shining Armor, due to being a Weirdness Magnet. Not only is he being chased by a cosmic entity trying toerase him from existence, he has an insane Parody SueGeneral Ripper out to make his life a living Hell, all for things completely out of his control. Even discounting the weirdness, he's still got to spend about two years away from his beloved little sister and family while he's living with the guilt of his uncle Cool Sun sacrificing himself for his sake. Did we mention the Wedding hasn't even happened yet?! He and Twilight would already have a lot to talk about.
At this point, the crew probably all count as well, given the drama, pain, and conflict that they were put through over the past year.
Bon Bon during the Wedding Arc. Not only does she end up getting dragged into the battle with the Changelings, she discovers her beloved 'twin sister' was actually a Changeling and she never had a sister.
Woobie, Destroyer of Worlds: The Mane 6 in the epilogue timeline. Being brainwashed to do Discord's work does not make them happy ponies, although Fluttercruel and Angry Pie's murderous actions caused them to cross the Moral Event Horizon, thereby preventing them from being sympathetic again.