Alas, Poor Scrappy: Diamond Tiara probably never got the Character Development her canon counterpart did, and she probably never made the HeelFace Turn her canon counterpart did either, but it's still a little hard to believe she did anything to get the death she got.note She killed herself to keep the other inmates from killing and eating her.
Littlepip as a Villain Protagonist. Several of her actions can be seen as morally questionable as she can be pretty ruthless towards her enemies. The story itself even acknowledges this viewpoint, with Red Eye explaining how they are Not So Different. Fans with the most extreme versions of this interpretation may view the character as a Designated Hero.
Good intentions or not, Velvet Remedy can be seen as a self-righteousegotisticalbitch, who mocks and insults Littlepip and her other companions for their actions no matter how justified they may be. Even after her Character Development, she is shown to still have traces of this.
Calamity is intended to be a Boisterous Bruiser that gets a little overexcited in a fight, but his frequent borderline Squee! reactions to finding increasingly dangerous weapons can come off as disturbing.
Anti-Climax Boss: Nightseer gets quite a bit of buildup. Littlepip kills her within the span of a single paragraph.
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.
Darkness-Induced Audience Apathy: The dark setting and questionable morality of the protagonists make the story rather hard to read for some people. It says a lot when fanfic critics have called it more depressing than the actual Fallout canon. Some say that what makes Fallout as a series really tick, is that despite its bleak setting, there has always been a spec of cautious optimism and hope at its core. Despite the inherent optimism in the story and the bittersweet happy ending, some readers contend that the fic has failed to capture this feeling, portraying instead an overly grim dark setting.
Many of the cast of Friendship is Magic die horrible and arguably pointless deaths.
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.
Aa well as a massive bubble like shield surrounding Canterlot.
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 Pies only regret was that she couldnt be everywhere helping all the troops all the time!" Too Many Pinkie Pies takes on an almost eerily similar premise.
Learning in season 5 how dilapidated and fallen to poverty Griffonstone became and how griffons are Only in It for the Money, it's no surprise they were depicted as Equestrian mercenaries.
Also from season 5, it is revealed that Pinkie Pie actually has a massive underground vault full of detailed files on everypony in town. Cataloging everything they like, dislike, preferred types of parties, etc... Pinkie Pie has indeed been watching you, FOREVER!
Then comes the Season 5 finale. First we see an alternate timeline where war has altered Equestria. The entire population putting all their effort into supporting the war effort, even a Future Badass Rainbow Dash with a cybernetic looking wing. Then the finale alternate timeline was Equestria turned into a vast, empty, barren wasteland.
Fluttershy gets turned into a tree in this story because she came into contact with a magical flower. In A Health of Information this not only nearly happens to her, but it's revealed that there's a disease that causes ponies to turn into trees!
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. According to an Equestria Daily mod, Fallout Equestria simply came out at the right time, when the show was partway through the first season and there weren't very many quality control restrictions on fics, to the point where if FO:E were submitted later, it never would have passed moderation.
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.
It Was His Sled: Who doesn't know that Steelhooves dies and Littlepip ends her journey forever in the SPP pod?
Just Here for Godzilla: Some fans only read the story for the large amount of World Building and backstory, finding the main narrative less compelling than the events that shaped the present. This may account for the spinoff fanfiction, where writers are free to make their own cast of characters that are doing their own thing.
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 (and justifies) 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.
They Wasted a Perfectly Good Plot: Wait, so a hellhound got turned into a pony? I bet you can't wait to see what its life will be like now! ...Oh wait, chances are its dead now.
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.