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.
Anti-Climax Boss: Olive Branch's poorly thought out plans fall apart and Celestia easily arrests him.
Broken Base: There are some people who believe that Darth Link didn't go far enough. One such fan went on to write Faith and Doubt, a much, much darker and tragic take.
The final events of Chapter 18 of Families weren't received well. Specifically, several felt 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 "anti-Celestia conspiracy" subplots. Darth Link has expressed surprise that no one saw this coming, considering 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.
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 conditioning described in A Clockwork Orange.
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 Slice of Life stories.
Complete Monster: Discord from the story Metamorphosis was the one who murdered the founders of Equestria and was responsible for Chrysalis' Start of Darkness. He manipulated a disgrunlted 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, transforming the rest of them causing them to fall apart and die, and made the two survives 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 "the Powers of an Alicorn", and the two of them turn Equestaria into a chaotic hellhole for thousands of years.
Darkness-Induced Audience Apathy: 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 jumped ship altogether when the followup Direction was posted with that tag to begin with, indicating that both tone and content had left the Original Flavor that attracted them permanently behind. (Ironically, Darth Link only added the tag as a preemptive response to these objectors and has since removed it.)
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.
Celestia laughing at Olive Branch's desire for immortality may be awesome, but it becomes a bit sombering when you realize she has verygoodreasons for despising her own immortality outside of the obvious.
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.
Malignant Plot Tumor: The Olive Branch story thread in Families 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. 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 more or less the entire second half of the story, while the "personal troubles" were wrapped up (or tied in to Olive Branch) midway through.
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.
Villain Sue: 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 god-princess and seemingly nopony being willing or able to take reasonable action against him. 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 his real goal was something that had already been revealed to be impossible.