* AntiClimaxBoss: [[spoiler: Olive Branch's poorly thought out plans fall apart and Celestia easily arrests him.]]
* BrokenBase: Whether the CerebusSyndrome is a good thing or not.
* CompleteMonster: [[GreaterScopeVillain Discord]] from the story ''Metamorphosis'' murdered the founders of Equestria and was responsible for Chrysalis's StartOfDarkness. He [[ManipulativeBastard manipulated a disgruntled pegasus]] into attacking the meeting discussing the unity of the ponies, offering her the powers of an Alicorn and turning the Flutterponies into the monsterous Changelings for an army. They attacked the meeting, wiped out all guards to replace with the Changelings, forced Commander Hurricane to shoot her friend Pansy, transformed the rest of them causing them to fall apart and die, and made the [[WhoWantsToLiveForever two survivors, Celestia and Luna, immortal so they can never join them in death]]. After this he has the Changelings turn the pegusus into Queen Chrysalis explaining that he had promsed her "[[ExactWords the Powers of an Alicorn]]," and the two of them turn Equestaria into a chaotic hellhole for thousands of years.
* DarknessInducedAudienceApathy: After several readers expressed dissatisfaction with the dark Olive Branch and Scootabuse storylines in ''Families'', to the point of forcing a Dark tag onto the story, they [[ScrewThisImOuttaHere jumped ship altogether]] when the followup ''Direction'' was posted with that tag to begin with, indicating that both tone and content had left the OriginalFlavor that attracted them permanently behind. (Ironically, Darth Link only added the tag as a preemptive response to these objectors and has since removed it.)
* FanonDiscontinuity: Many of those who aren't fond of how the series gets DarkerAndEdgier treat ''Post Nuptials'' as a stand alone fic.
* FranchiseOriginalSin: While ''Post Nuptials'' was praised for it's [[{{WAFF}} idealistic tone]], it [[{{Foreshadowing}} hinted at darker themes]]. ''Metamorphosis'' showed plenty of darkness, but being a side story, didn't affect expectations for the main series. Come ''Families'', the Olive Branch story thread irked quite a few readers who had come into the story following the [[ExactlyWhatItSaysOnTheTin various 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. in response to a comment 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 second half of the story'', while the "personal troubles" were wrapped up [[spoiler:(or tied in to Olive Branch)]] midway through. Once it seemed ''Direction'' was going to [[DarkerAndEdgier continue the trend]], many reader abandoned the series for [[TheyChangedItNowItSucks loosing the idealism that was its big draw]].
* HarsherInHindsight:
** Rainbow Dash's total breakdown at Twilight [[spoiler: seemingly]] [[EasilyForgiven forgiving everybody with no grudge whatsoever]] was already bad enough. It gets even worse when she confesses to Soarin in her chapter that she really, ''really'' wanted Twilight to brand her and the others as complete idiots and make them move mountains to earn any amount of forgiveness for what they did.
** Spike total guilt about the rehearsal incident in ''Post Nuptials'' makes even more sense when you find out in ''Families'' about all of the FantasticRacism he endured in early childhood, how Twilight always defended him, was the only one who was always there, and made him feel like he was special. No wonder why Spike views her as a mom.
*** Spike also at one point complained to the CMC that [[Recap/MyLittlePonyFriendshipIsMagicS2E10SecretOfMyExcess while he was growing due to his greed]] the doctor told Twilight to try the vet. Spike was hurt by this because as he said "(he's) not a dog!" Then in ''WesternAnimation/MyLittlePonyEquestriaGirls'' he really does become a dog. Once the Nuptialverse gets around to Equestria Girls, Spike himself suffers a small HeroicBSOD once he realizes his transformation, and how it limits how he is able to help Twilight.
** 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 [[CruelMercy very good reasons]] for despising her own immortality outside of [[WhoWantsToLiveForever the obvious]].]]
** A common complaint about the rift between the Humane 5 in Equestria Girls before Twilight mended it was how it was based on weak misunderstandings aimed at a specific person. ''Through the Mirror'' has the rift between the group even ''WORSE'' because Sunset engineered rumors that drove them apart (one of them got Fluttershy and Rainbow harrased by students, another nearly got Rarity expelled) and none of them can even look at the other girls now.
* 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. 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.
** Relatedly, given how much [[AdaptationalVillainy eviler and serious Discord was here]], that his defeat (in the middle of laughing at the Princesses efforts to stop him when they sicced the Elements of Harmony on him) so perfectly caught [[Recap/MyLittlePonyFriendshipIsMagicS4E2PrincessTwilightSparklePart2 how they defeated him in canon]] (down to Discord leaving behind something that would cause trouble 1000+ years later) is rather miraculous.
%%* JerkassWoobie: Queen Chrysalis, of all people, in "Metamorphosis".
* 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]].
** Chrysalis selling out Equestria to Discord for personal power.
* ToughActToFollow: ''Post Nuptials'' received near universal acclaim, which its sequels, and Darth Link's subsequent works, have had a hard time living up to. Many other Canterlot Wedding {{Accusation Fic}}s have also been critiqued as mere whining compared to the [[{{Deconstruction}} thoughtfulness]] and [[{{WAFF}} satisfying resolution]] of ''Nuptials''.
* {{Wangst}}: The group's JerkassRealization is one thing but their constant beatings over themselves send them over the edge over this.
%%* TheWoobie:
%%** Spike during "Families"
%%** Scootaloo.