* AntiClimaxBoss: [[spoiler: Olive Branch's poorly thought out plans fall apart and Celestia easily arrests him.]]
* BrokenBase: There are some people who believe that Darth Link didn't go far ''enough''. One such fan went on to write ''FanFic/FaithAndDoubt'', a much, ''much'' darker and tragic take.
** The final events of Chapter 18 of ''Families'' weren't received well. Specifically, several felt [[spoiler:the reveal that Olive Branch was present and watching Speedy Delivery abuse Scootaloo]] was an extremely dark and abrupt turn that clumsily combined the "Scootabuse" and "[[spoiler:anti-Celestia conspiracy]]" subplots. Darth Link has expressed surprise that no one saw this coming, considering [[FridgeBrilliance it explains why Scootaloo's parents always want her out of the house]]. It's also worth noting that even the people who DID see it coming thought it could have been handled better.
** As of chapter 24, some readers are starting to get tired of the [[ArcFatigue constant cliffhangers and last minute escalations of the conflict]], as well as how several characters constantly get [[TheWorfEffect worfed]] for the sake of the villains. It got to the point that Darth Link ended up [[LampshadeHanging lampshading]] the cliffhangers in the author's notes for chapter 25: "See? No cliffhangers."
** In general, whether the CerebusSyndrome is a good thing or not.
** [[spoiler: Olive Branch's punishment by Luna had a few fans worried about how much power the Princesses showed, not helped by its similarity to the [[HeelFaceBrainwashing conditioning]] described in ''Literature/AClockworkOrange''.]]
** If you check his reviews, you'll find fans of his that flat out tell him they don't like his adventure stories and to let him know they want him to stick to SliceOfLife stories.
* CompleteMonster: Discord; in this story he's a gleeful, unrepentant, murderous psychopath who's ''guaranteed by the Keeper herself'' to give Twilight nightmares worse than the ones she already has if she knew what he has planned for her. Given that he [[spoiler:horrifically murders all of Equestria's founders as well as Celestia and Luna's entire family (and then makes the latter two immortal so they can never join their loved ones in death), all with a big goofy smile on his face]], it's safe to say that at least the characters have good reason to think he's this.
* HarsherInHindsight:
** Just about everything Scootaloo does in the canonical series becomes this as more of her family situation comes to light in ''Families''.
** Pinkie's {{Flashback}} in "[[Recap/MyLittlePonyFriendshipIsMagicS1E23TheCutieMarkChronicles The Cutie Mark Chronicles]]" after it's revealed that she drastically changed certain details in order to avoid upsetting the CMC.
** Fluttershy's TheReasonYouSuckSpeech to Pinkie Pie in "[[Recap/MyLittlePonyFriendshipIsMagicS2E19PuttingYourHoofDown Putting Your Hoof Down]]" was harsh enough already, but when Fluttershy learns how it reminded Pinkie of [[spoiler:her parents' ''real'' reaction to her cutie mark]], it becomes even worse.
*** And Iron Will, who started his coaching to help ponies not be bullied like he once was, found out that Fluttershy was far from the only pony to go overboard with his teachings and many have become bullies themselves.
** [[spoiler:Celestia laughing at Olive Branch's desire for immortality may be awesome, but it becomes a bit sombering when you realize she has [[LastOfHisKind very]] [[SoleSurvivor good]] [[ParentalAbandonment reasons]] for despising her own immortality outside of [[WhoWantsToLiveForever the obvious]].]]
* HilariousInHindsight: In this story, Discord is described as a creature so cruel and sadistic that [[Recap/MyLittlePonyFriendshipIsMagicS2E1TheReturnOfHarmonyPart1 his]] [[Recap/MyLittlePonyFriendshipIsMagicS2E2TheReturnOfHarmonyPart2 actions]] shattered Fluttershy's worldview that showing others kindness is the key to bringing out the good in anyone. [[spoiler:Then "[[Recap/MyLittlePonyFriendshipIsMagicS3E11KeepCalmAndFlutterOn Keep Calm and Flutter On]]" aired and showed Fluttershy doing just that with Discord. Needless to say, it immediately became clear which season 3 episode Darth Link would be ignoring for this continuity]].
* JerkassWoobie: Queen Chrysalis, of all people, in "Metamorphosis".
* MalignantPlotTumor: The Olive Branch story thread in ''Families'' irked quite a few readers who had come into the story following the various [[ExactlyWhatItSaysOnTheTin family issues]] only to see most of them pushed aside in favor of what they saw as a trite and/or unrealistic conspiracy/thriller angle. Bizarrely, in response to a comment on the sequel about the plot thread's perceived weaknesses, Darth Link justified them with it just being a side plot and wanting to "keep the focus on the personal troubles", despite it ''being'' the entire last quarter of the story and providing the majority of the conflict beforehand, while the "personal troubles" were wrapped up ([[spoiler:[[ArcWelding or tied in to Olive Branch]]]]) midway through.
* MoralEventHorizon:
** Speedy Delivery might not have that much support after he [[spoiler:steps on Scootaloo's wing]].
** Olive Branch, while not a good guy to begin with, crosses this line when he [[spoiler:has Twilight attacked and kidnapped]].
* VillainSue: Olive Branch came across this way to a good deal of readers due to the apparent ease with which he could turn much of the populace of Equestria against their immortal [[GodEmperor god-princess]] and seemingly nopony being willing or able to take reasonable action against him. [[spoiler:The climax of ''Families'' subverted it when he overplayed his hand and found he had ''vastly'' underestimated Celestia and the Mane Six- not to mention that [[ImmortalitySeeker his ]]''[[ImmortalitySeeker real ]]''[[ImmortalitySeeker goal]] was something that had already been revealed to be impossible.]]
* TheWoobie:
** Spike during "Families"
** Scootaloo.