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.
Alternate Character Interpretation: Diamond Tiara and Silver Spoon. They're portrayed as well meaning in nature, but their approach to caring involved a drill sergeant approach to others, riling them up in an effort to make them succeed at what they try to do.
Arc Fatigue: The current storyline from chapter 53 on is succumbing to this. Plot advancement has been sacrificed in the name of painting a very detailed, but very bleak picture of what the characters are going through, as they're targeted for attack by some unknown villain.
Base Breaker: The coverage of the Mare Do Well event is this to the readers. Either Rainbow Dash is correct in being angry at her friends for their betrayal, or she's incredibly dense and selfish for not seeing that they were going to desperate lengths to try and help her when she didn't know she needed help.
Cry for the Devil: Chrysalis. Just Chrysalis. What started off as being a stereotypical villain plot, somehow morphed into being a desperate attempt at saving her people/species from extinction, and everything going horribly, horribly wrong.
Darkest Hour: Ponyville is in genuine peril, our heroes have absolutely no idea what's going on, whoever the Big Bad is apparently doesn't fear three of the strongest beings in existence, and said Big Bad has the ability to target a pony's own memories. If the current storyline doesn't qualify then I don't know what does.
Derailed for Details: The author seems to draw a sadistic level of pleasure from filling each chapter with loads and loads of details about all manner of things, even if they have no relevance until several chapters later on.
False Friend: Ulquiorra intends to invoke this trope in chapter 35 and onward, believing that if the ponies believe he's fully committed to the idea, they'll leave him alone, and focus on helping him learn whose threatening Equestria. Unfortunately his plans backfire by unanticipated developments, and the friendships developed that he didn't understand to begin with, have unintentionally been strengthened.
Godzilla Threshold: Crossed with extreme prejudice. Celestia has taken the threat to Equestria so seriously, she's asked Ulquiorra to go back to his old ways.
I Knew It: Ulquiorra with the Cynacism beating Idealism, over the course of his time serving aizen and in Equestria he has seen friendship.
Used as a tool to get Orihime to Huecco Mundo, Bring 5 people to Huecco Mundo only for nearly all of them to die, Get Ichigo killed by him twice, Fail in being used to stop a dragon he nearly had to kill to protect the mane 6, abandoned to prove a point about arrogance when told about the "Mare-do-well" incident, clouding the ponies from realizing fluttershy was replaced, used as a control mechanism both by himself and Rarity, be broken by mind raping powers with Rainbow Dash.
Nightmare Fuel: While as Nightmare Moon, Luna was still fully conscious of what was going on around her, able to observe and see everything Nightmare Moon was doing with her body, and unable to stop it. She had to watch as the entity possessing her body killed and ate foals.
The audience being lead to believe that Fluttershy was being murdered, when in reality it was a changeling in disguise.
The whole of Rainbow's description of her being raped by the other elements.
Oh, Crap: The reader's reaction to the ending paragraph of Chapter 58.
Paranoia Fuel: Surprisingly Ulquiorra embodies this trope rather than the ponies. He believes that there's something sinister loose in Equestria, out to kill the Mane Six.
Ulquiorra's actions with ending Cupid's suffering may very well qualify, as he explains how simply waiting for nature to take its course would be extremely cruel.
Ulqiorra's interactions with the CMC in chapter 51 would also qualify. It starts with him stopping Sweetie Belle from crashing into the ground, and eventually ends with him giving Scootaloo some advice on how she may increase her chances of learning to fly.
Rousseau Was Right: Ulquiorra is at the very least walking the line on this one. He's shown that he can be kind towards others just as easily as he can be lethal, and all without breaking stride. In chapter 44 he not only aids in the rescuing -and subsequent transporting- of injuries ponies to the hospital, he also spends a considerable deal of time making the case for why a poisoned foal by the name of Cupid should be euthanized quickly, rather than be allowed to die slowly and painfully. He even opts to do the dirty work himself, so no one else will have to deal with the guilt.
Shell-Shocked Veteran: This trope definitely applies to Ulquiorra. The introduction is practically word for word to his character; he's seen and done things that no amount of therapy is going to heal (not that he actually cares) and doesn't have much care for those around him, so long as they're staying safe.
Team Dad: Ulquiorra has brief (very brief) moments of this trope, primarily when he's dealing with the CMC and other foals.
Teeth-Clenched Teamwork: Anytime Ulquiorra has to work with the mane six on anything of genuine importance, like the safety of Equestria. He has little tolerance for their emotional nonsense, and they abhor his utter brutality and straightforward approach to facing a threat. And that's just when things are in the nonlethal category.
Diamond Tiara and Silver Spoon having to work alongside the Cutie Mark Crusaders would certainly count as well.
Unreliable Expositor: Ulquiorra could be this involving him accepting friendship. When accused by rainbow that his apology wasn't sincere earlier, he responded flatly that it wasn't. That could be taken as a sign that he isn't fully committed, as no one has asked him if he has been sincere about accepting friendship.
Woobie, Destroyer of Worlds: With how the ponies see him, saddened by his social darwinsts, violent, and empty past, but seeing how strong he is this would be Ulquiorra from most of the other character's perspective.