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.
Arc Fatigue: Even the story's fans are starting to wonder exactly when the story is going to end. Project Horizons is now longer than the original story, with no ending in sight.
This is averted after the Thunderhead arc beginning in chapter 58. Many of the big mysteries are starting to be answered. Word of God has assured readers the ending's in sight. And as of chapter 70, Somber looks to be delivering on that promise as the climax looks to going off at any moment.
Base Breaker: Goldenblood. While some readers agree with the author's intentions that the character should explain the state of wartime Equestria, others feel that he lessens the original characters and events by stealing away the responsibility for their actions.
On a meta level, the story itself. Love it? Hate it? Indifferent? Either way, just mentioning Project Horizons is grounds for a Flame War in some circles. Doesn't help BJ and Pip tend to get compared with each other a lot.
Complete Monster: A number of them, though most of them do have a tragic backstory behind them. The only real one so far would be Brass, the manticore-pony hybrid who was around during the war and was responsible for Deus becoming what he was. She's actually so bad that Blackjack reacts with glee at finally being able to kill someone that she doesn't have to lose sleep over, and actually asks her if she eats babies or other monstrous activities.
Deus Angst Machina: Virtually every named character suffers (or has suffered) life-changing trauma, often of a sexual nature. This extends to foals, with child rape alluded to as early as the second chapter. Each of the main characters have their lives and bodies ruined several times in the course of the narrative.
Boo, the allegedly soulless clone that Blackjack befriends in Hippocratic Research, recieved fan art and an independent Character Blog within days of her first appearance.
Charity, a surprisingly shrewd merchant filly. She's both cute and amusingly greedy, practical, and still young enough to be a Crusader. Yet nevertheless so dependable and fair as to earn most of the Hoof's respect regardless.
The reason why Stable 99's recycler wasn't able to get rid of the Raider Virus? It's based on Creutzfeldt–Jakob disease and Mad Cow Disease which are caused by prions. Prions are proteins that act like viruses but cannot be destroyed short of destroying the material that they are contained in.
The reasons for Glory's mother becoming a dashite aren't really explored, save for the fact that she was originally from the surface and therefore unpopular with the Enclave. Then you consider that Glory mentions having four sisters, the youngest being a pair of twins. The Enclave has strict limits on breeding due to population and resource concerns - as a mother of five, as well as an outsider, it's no wonder that Dawn caught a lot of flak. Her husband's rank and political influence were probably the only things keeping her from being banished (or worse) sooner.
P-21 served as a breeding stallion in Stable 99 for over ten years. It's unlikely that Scotch Tape was his only child. And if he did have any other children, Blackjack killed them all in the massacre of 99.
Goliath, the enormous train-pulling pony that Blackjack and friends meet at the beginning of Chapter 36, is mentioned to have gotten his incredible size from an encounter with Killing Joke. BJ notices a grievous scar on Goliath's mother's belly, and suspects that the injury was caused by a landmine. She fails to consider another, somewhat darker possibility.
Every single pony that has died in Hoofington, including those that Blackjack and company have killed, has had their soul sucked into the swirling vortex of endless torment and despair that orbits around the fallen star that lies at Hoofington's core. Every single one. Count them.