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 turn, Velvet Remedy (while she may have good intentions) can be seen as self-righteousegotisticalbitch, who mocks and insults Littlepip and her other companions for no good reason. Even after her Character Development, she is shown to still have traces of this
Arcadian Interlude: The sudden pornographic scene in chapter 20.5 (a "deleted scene" chapter by another writer which is treated as potentially canon by the original author).
Awesome Music: A fan performed this piece in honor of Littlepip, the first in what will be a line of several FO:E inspired songs. The instrumentals and vocals are excellent, and the lyrics fit Littlepip's struggles throughout the story perfectly. "I'm sick and tired, of all this fighting. Not sure if this blood is mine..."
A good number of brony musical artists have composed songs inspired by Fallout: Equestria, including dozens of songs available on YouTube and even music featured on the "Balloon Party" album series.
The story depicts Ditzy Doo as unable to talk because her tongue was cut out. Later, the referring to the character in the show as Derpy, combined with her voice, lead to backlash from Moral Guardians for the Unfortunate Implications, resulting in her voice being changed and likely making it so she won't be getting another voiced part anytime soon.
Hilarious in Hindsight: Watcher is a mysterious gravelly-voiced nigh-omniscient observer who communicates by hijacking floating robots - just like Ulysses in Lonesome Road, which was released several months after Fallout: Equestria started.
Littlepip thinks the name "Pipsqueak" would be ridiculous. Then an actual character named Pipsqueak appeared in the show.
And what nickname did Zecora give him? Little Pip!
All of the magic spells that Kkat came up with before season 2 even started, including memory transfers, bypass spells, and self levitation.
Now add in the harnesses used to hold the lances for Crystal Ponies while jousting, which resemble very early battle saddles.
Zecora crafts a potion that gives zebras bat-like wings. Two months later, the episode "Luna Eclipsed" introduces bat-winged ponies.
Why did the Everfree Forest mutate into a much more horrible and deadly place when it was never hit by a megaspell? Because the Elements of Harmony were removed, and their presence in the Forest had been holding the horrors back... much like the revelation in the Season 4 premiere.
Inspiration Manifestation confirms dragon tactic of "eat it" for disposing of hazardous magical items.
Twilight's Kingdom shows extremely destructive spells similar to balefire bombs, complete with mushroom clouds.
In the chapter The Moral of the Story, Pinkie Bell makes the remark that "Pinkie Pie’s only regret was that she couldn’t be everywhere helping all the troops all the time!" Too Many Pinkie Pies takes on an almost eerily similar premise.
Hype Aversion/Hype Backlash: This is easily one of the most famous Friendship is Magic fanfics out there. It has fan art, fan music, there are fan games being made for it including Fallout 3 mods, and it has inspired dozens of spin-off fics. Does it deserve all this attention? Not everypony would agree.
Littlepip converses with Watcher while she's wearing raider armor - the only thing she could find at the time - and Watcher fails to warn her about the negative connotations which later lead to a near-fatal misunderstanding.
The first alicorn LittlePip meets decides to stand perfectly still and hurl taunts while Pip puts everything she has into casting a powerful spell. Naturally, that spell kills her.
In the Balloon Orb, Pinkie Pie's refusal to inform herself as Pinkamena through the soul mirror of the oncoming apocalypse when LP tries to warn Pinkamena through her, stating that the knowledge is a secret despite this event prompting real world Pinkie Pie to create and plant the mane six memory orbs for LP to find later in order to fix the world. Depending on how one takes this, it could actually be Fridge Logic as Pinkie Pie's future reading abilities may have shown her no other clean outcome possible except to let the world melt and have LP clean up after.
Which now makes sense, due it being made clear that Equestria time travel runs on the Stable Time Loop. Nothing could be changed about the past.
In his planning, Red Eye somehow forgets one way LittlePip might use her signature ability - extremely powerful telekinesis - which leads to his humiliating defeat during the final confrontation between them. He immediately lampshades the moment.
Internet Backdraft: Quite a bit, mainly due to combining MLP with something as dark as Fallout, as well as the seemingly meanspirited way the Mane Six and their friends met their ends.
Iron Woobie: Ditzy Doo. When the megaspells dropped, she was caught at the edge of one, which turned her into a Ghoul. She's spent the next 200 years doing whatever she can to survive, with the always present possibility that her mind will degrade to the point where she becomes little more than a mindless beast. This also has the effect of making surviving ponies reluctant to go near her, since nopony wants to be around when a zombie flips out. But even with all this, she is still friendly and helpful, to the point where Littlepip calls her the nicest pony she's met in the wasteland, and later becomes the new Element of Laughter.
The Steel Rangers invading Stable Two and attempting to slaughter everypony in it just to get at the pre-war technology it holds.
The Enclave attempting to destroy Friendship City just to kill one Dashite (prior to the attack commencing one of them even shoots a terrified filly who was trying to get away from Littlepip, then attempts to justify it by saying that they couldn't take any chances.)
Littlepip treats her massacre of everypony in Arbu as this.
Strawman Has a Point: Red Eye's propaganda states that all races of pony are equally important. He seems to consider the opposition that earth ponies are the best, which seems laughable. His opposition's points seem to be better than his, and then you realize that the pro-earth pony Stable he's from invented cybernetic implants and cured old age with only the tiny population of one Stable.
Ugly Cute: Ditzy as a ghoul, who despite looking and smelling like a body that's been in the sun for a few days, is one of the most friendly and genuinely helpful ponies in the story.
The Woobie: Get out yer hankie, it's easier to count the characters who aren't this trope.