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.
In addition to the standard "characters are far different from their original characterizations for the sake of humorous juxtaposition" found in abridged series and similar web remixes, "Dragone Baby Gone" suggests that Rainbow Dash and Applejack got their Elements mixed up. This references a common joke in the fandom that they often (in the earlier seasons) seem to suit one another's elements more than their own.
Fluttershy's father may not be as evil as he's made out to be, seeing as how Fluttershy seemed more concerned about missed softball practices than being left out in the frozen tundra and being eaten by African Ants that might not be able to survive in such temperatures. Considering her "element" is deception, it's possible she's lying to gain sympathy (that's not to say he wasn't abusive, but setting one's toys on fire is a different kettle of fish than abandoning them in the wilderness).
Crack Pairing: Twilight and "Francis Sparkle" (Shining Armor). Even if unrelated, they're still siblings.
Crosses the Line Twice: Their treatment of Raincloud, the Sooty Snark Evaders blinding Babs, the "Snowblind" segment and Twilight abandoning Cadence in a cave to die of dehydration in order to marry her brother.
Sweetie Belle. Even as a robot, people find her utterly adorable.
Silver Spoon and Diamond Tiara are far more popular here than they are in the show itself. In the case of Diamond Tiara, this isn't saying much, but fans have really latched onto Silver Spoon, especially after Griffin created a spinoff series about her.
Fandom Nod: The Enterplay Series 2 Sweetie Belle card includes the line: "But her cutie mark acquisition program hasn't seen much success".
Fridge Brilliance: During "Sweetie's Big Race" in the fifth episode, Rarity and Sweetie Belle enter the chicken coop, which has "One egg per sentient life form" written on its side. They come out with a single egg because Sweetie Belle is a robot.
Also, Fluttershy initially doesn't want Pinkie Pie to sing her a song in "Dragone Baby". But then all the sudden, she gets over her fears and jumps the cavern. Why? Because why wouldn't a girl upset about confronting her abusive father feel better after hearing about having both your parents die.
Why doesn't Applejack like Pinkie's song in "Cherry Bomb"? Because its lyrics ("When you're rife with devastation", "And your loved ones have been mangled", etc) are reminding her of the bomb.
Twilight acts in an explicitly horrifying way during episode 8, but not only has her nature been suggested in all the earlier episodes ("You wouldn't want to end up like Twilight's old friends in Canterlot, would you?") but Cadence remarks on the flat characterizations that Ponyville approves of. One wonders whether it's Twilight's doing or if it goesdeeper.
A newspaper mentions Newt losing a second eye and all of his limbs in a "baking accident". Perhaps Pinkie is not as sympathetic as one may think...
Hilarious in Hindsight: So many things from this series have turned out to be canon or at least similar to scenes that would appear on the show that people have wondered if Jenny and Griff secretly work on the show in some capacity, or get leaked info from people who do. Thus far:
In "Cute From The Hip", there's a joke about Apple Bloom earning a spinning cutie mark. In "The Cutie Pox", one of the cutie marks she got was a spinning-related one.
It also showed that Pinkie Pie's parents were gypsies and that she's been trying to carry on the family tradition. Cue a scene of her as a fortune teller in "It's About Time."
Twilight Sparkle mentioned having a brother in "Neigh, Soul Sister". She really does!
Speaking of Equestria Girls, Twilight's feelings for a certain blue-haired rocker boy is all the more entertaining now.
Even the parody song "The Convention" turns out to be eerily prescient — Rarity is said to have sewn her cosplay outfit "last night in [her] hotel room." Season four features an episode where she actually does that. Using stuff she stole from the hotel's own décor, to boot.
Their Equestria Girls parody has a brief moment where a characters says "Let's start a rock band!". This appears to be the plot of Equestria Girls 2.
"For Whom the Sweetie Belle Toils" has Sweetie fall down stairs like a slinky.
Continued in "Cute from the Hip," where Apple Bloom claims that Fluttershy told her that Pinkie Pie has "evil gypsy powers and the voluminous hairof a temptress."
"Cute from the Hip" also implies that Diamond Tiara has a thing for Apple Bloom, which she tries to hide by teasing her. Silver Spoon also wants to be more than friends with Diamond Tiara, but is aware of her feelings for Apple Bloom and spurred to jealousy.
Painful Rhyme: Several in "Gypsy Bard", such as "tilts it <-> resilient", "filly <-> city", "orphanage <-> wanna fit in".
"How Applejack Won the War" also has many, like "just wait and see <-> all we need", "farm <-> barn", and "battleship <-> honeycrisp".
Parody Sue: Princess Notevil Goodpony (Princess Cadance's identical twin sister) is a world-peace advocate, organ donor, elected ruler of her own country, and Only Sane Mare in a Crapsack World. Unfortunately, this doesn't grant her an ounce of protection from the Crapsack World.
The Scrappy: Nearly everyone. Special mention however goes to Twilight, due to being a Manipulative Bastard, being an Alpha Bitch, and generally being cruel to Spike, not to mention killing Cadence so she could date her own brother.
Pinkie as well, given she's treated as a nut and a witch, as well as the fact her parents died. "Pinkie's Brew" is about her being so desperate to reunite with her parents that she's willing to fudge the space-time continuum to do it. She succeeded.
Rarity was screwed up pretty badly by the war, if Sweetie Belle's statement about how she spends every Veteran's Day is any indication. Not to mention the fact that she made a sweater that was specifically designed to hug her.
Luna/Molestia. She's so socially awkward and sounds so pitifully lost.
Luna:(to the creepy statue outside Ponyvile) Oh statue, you are my only friend...
Raincloud. She never fit in with the ponies, and made a Heroic Sacrifice in her first and only appearance.
Cadence, the show's Only Sane Mare who has to deal with her soon to be husband going through Flanderization thanks to his sister's presence, and Twilight constantly trying to replace her as the bride. She succeeds, and leaves Cadence in the caves beneath Canterlot to die.
Woobie, Destroyer of Worlds: Fluttershy. Based on what little information is given about her childhood, if you peeled away the layers of Antichrist, you'd find a profoundly damaged young woman.