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.
Dude, Not Funny!: See below. Applejack was originally going to be homophobic to the point of reacting like someone with arachnophobia would, for example. Readers were relieved when this idea was thankfully scrapped. It doesn't help that many fanfiction writers use Applejack and/or her family as token homophobes a lot, something which pretty much anyone is understandably annoyed by.
Jerk with a Heart of Jerk: Gilda. Big time. She threatened to rip Fluttershy's throat out if she even so much as batted her eyelashes at Rainbow Dash. Whether an exaggerated threat or not, it was still pretty deplorable of her. For no good reason other than being a Clingy Jealous Girl
Les Yay: Rainbow Dash and Fluttershy throughout the ENTIRE story. It doesn't help that Fluttershy has a crush on Rainbow. Even before she is no longer afraid of her love for Rainbow and accepts her feelings completely. The story is full of sweet and shippy moments between them, including a Near Kiss. YMMV on the ending. While it makes sense, it did still leave shippers of the pair with a lot to be desired.
Mood Whiplash: All throughout, the story is loaded with comedic elements. Chapter seven contains a sad backstory, which explains a lot of things in the present time.
Nightmare Fuel: While it's meant to be played up for laughs; it's revealed that Angel created all kinds of elaborate and dangerous traps throughout the Everfree Forest. Despite that it's with the intention of protecting Fluttershy, considering how close she lives to the forest, it's pretty creepy. You have a rabbit, less than a foot tall, who can build traps that not only capture and contain victims, but KILL them. He even has a secret box filled with all kinds of plans and blueprints. One of which is about how to KILL your enemy. It's no wonder he was jokingly referred to as a cross between Bugs Bunny and Jigsaw.
Obligatory Joke: A prank featuring Lyra Heartstrings. It's based on her meme of being obsessed with humans, despite that the story is meant to take place within the canon of the show. It also is a callback to G1 having seaponies. Readers are divided between it being funny and collectively groaning at the use of it.
Squick: Angel planting laxatives into Rainbow Dash's soup, to which she later ends up in the bathroom for. For a story rated E and not being graphic in detail; it isn't hard to picture the gross-out mental images of the scene. Especially since Fluttershy is by her side the entire time.
Tear Jerker: The reveal that, in her flashback, she was telling the story of her day to a picture of her mother, who had passed away.
The Woobie: Younger Fluttershy. Her mother passed away when she was younger, she was under the threat of Gilda because of her crush on Rainbow Dash, and was eventually abandoned by Rainbow. Made even worse because Fluttershy knew Rainbow wanted to tell her, but never did. On top of that, she was in love with Rainbow for a long time, but was always somehow out of reach despite being so close.
While things are certainly better in the present time, she still is a bit of one what with their emotional business remaining unresolved. She even breaks down into sobs in chapter eight when finally expressing to Rainbow Dash about how miserable and lonely she had been back then.
Even worse, when Fluttershy bore her soul about that, Rainbow proceeded to explain why she did what she did, making it sound like she just didn't care. Cut the poor girl a break!
Rainbow even qualifies in some ways. Despite that she does fight back against Angel, she inadvertently became his target due to the bracelet incident and was misconstrued as abusing Fluttershy. When she didn't even do anything wrong.
Even her own backstory offers an emotional tug of the heartstrings. It turns out she hated her life in Cloudsdale and Flight School, and wanted something different. The only thing about it that she ever truly liked was Fluttershy. She even chickened out telling her that she was leaving due to the fact that she knew she would be unable to leave her behind. She ended up doing so, and regretted it ever since. Despite that her life ended up just fine since then, she expresses genuine regret about how hard it was to do that to Fluttershy, especially now that she sees the true weight of it from her end.
Some may even argue that Angel, being a rabbit and somewhat justified in attacking Rainbow (when she starts fighting back, anyway), can be shades of this.
Token Homophobe: Averted with Applejack. She isn't exactly homophobic, it's more that she doesn't understand it, and doesn't believe Pinkie's claims of Rainbow and Fluttershy being a couple.
Souldin claimed that he originally wanted to make her completely homophobic to the point of fainting from freaking out, just for laughs. However, he was talked out of it when a few of his readers expressed justified distaste to the idea, as well as the fact that it happened a lot in fanfictions. He understood and scrapped it, deciding to take a more serious and realistic approach.
Souldin: Applejack’s discomfort concerning homosexuals was originally going to be played for laughs, having her as a homophobic but reacting more in the manner of an arachnophobia or claustrophobic; passing out, shrieking with terror or breaking out into shivers. I went with a more serious and sympathetic approach in regards to Applejack due to the slightly common occurrence of Applejack being depicted as outright hatefully homophobic.