Complete Monster: "Metamorphosis": Discord is far more malicious than his later redeemed canon self. He is first introduced offering the rogue Pegasus that will soon be Chrysalis a deal that, in exchange for her servitude, she will have the power of all three tribes. He then made a hidden fourth tribe of ponies, the Flutterponies, painfully transform into the monstrous Changelings so the Pegasus can have an army. After the Pegasus and her changeling army ambushed the meeting, Discord reveals himself and murders the tribe leaders and everypony in the building in unusually cruel methods. When the Pegasus was growing impatient and wondering when Discord would hold up his end of the bargain, he has the Changelings turn the Pegasus into their queen, explaining that he had promised her "the power of all three tribes". When Chrysalis protested, he tortured her and told her she should be grateful for what he did and that she didn't wind up like Celestia and Luna, who he casually revealed to have Forced to Watch as he murdered everyone blood-related to them before making them immortal.
Franchise Original Sin: While Post Nuptials was praised for its idealistic tone, it 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 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 (or tied in to Olive Branch) midway through. Once it seemed Direction was going to continue the trend, many reader abandoned the series for loosing the idealism that was its big draw.
Spike's total guilt about the rehearsal incident in Post Nuptials makes even more sense when you find out in Families about all of the Fantastic Racism 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 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 My Little Pony: Equestria Girls he really does become a dog. Once the Nuptialverse gets around to Equestria Girls, Spike himself suffers a small Heroic BSoD once he realizes his transformation, and how it limits how he is able to help Twilight.
Hilarious in Hindsight: In this story, Discord is described as a creature so cruel and sadistic that hisactions shattered Fluttershy's worldview that showing others kindness is the key to bringing out the good in anyone. Then ""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 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 how they defeated him in canon (down to Discord leaving behind something that would cause trouble 1000+ years later) is rather miraculous.
Speedy Delivery might not have that much support after he steps on Scootaloo's wing.
Olive Branch, while not a good guy to begin with, crosses this line when he has Twilight attacked and kidnapped.
Chrysalis selling out Equestria to Discord for personal power.
Tough Act to Follow: 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 Fics have also been critiqued as mere whining compared to the thoughtfulness and satisfying resolution of Nuptials.
