Acceptable Targets: In the story (and some of its spin-offs), humanity itself. The story itself is a huge one for the fanbase, and the Spacebattles Forums especially used to love bashing it for a while.
Anvilicious: Many, many, many of these fics are extremely unsubtle about how Humans Are the Real Monsters, and some Anti-Conversion Bureau fics are just as unsubtle about how the ponies are like a holier-than-thou version of the Borg (but worse).
Confirmation Bias: Many writers willingly gloss over the worse elements in Equestria (like the numerous Jerk Ass ponies, and the common monster attacks) in order to turn Equestria into a Mary Suetopia paradise.
Counterpart Comparison: Rampant xenophobia to the point where xenocide is seen as a good thing, and worshipping a God-Emperor (well, Empress) who leads them in their quest to destroy things not of them? Chatoyance's ponies bear more than a passing resemblance to the Imperium of Man (who themselves are an amalgamation of the worst parts of several historical regimes, such as the Crusaders, the Soviets, and the Nazis).
Death of the Author: The author of the original The Conversion Bureau, Blaze, wrote his story as pretty basic wish-fulfillment/theory about why Equestria doesn't have humans, with some accidental Humans Are Bastards implications. The genre inspired by the story takes it as a tract about how Humans Are Bastards and therefore need to be assimilated by the ponies, Borg style.
This quote from Twilight in the original was intended to be a joke but it's a lot less funny with the numerous stories that have the barrier being intentionally expanded as a means to force ponification.
Twilight Sparkle: "Now, I'm almost positive all of you are here because you want to become a pony. This is a fact. You don't come here because you don't want to be a pony, unless someone forced you at gunpoint, but that's a different story."
This statement is also a lot less amusing once you read through stories that have the PER in them.
Twilight Sparkle: "Our plan is to ponify you, the sooner the better. Expect this to happen when you least expect it."
The author's note in the Google Docs version is not quite amusing anymore now that there are tons of Conversion Bureaudark fics and war stories. Also became very ironic in a retroactive fashion.
Blaze (Author's Notes): "I've seen a lot of backstories written about how Equestria is simply a post-apocalyptic Earth set in the distant future. I decided to expand on it in a much less...grimdark fashion."
Harsher in Hindsight: In First Contact, the US Northeast, New York City in particular, is threatened by an incoming humongous hurricane. First Contact was published before Hurricane Sandy.
Never Live It Down: Thanks to some very ham-handed writing, Blaze, the author of the original fic, will probably never shake off people's perception of him as an absolute misanthrope. Likewise, the misanthropy laced first chapter is widely seen as being emblematic of the fic (and the entire 'verse) as a whole.
Overshadowed by Controversy: TCB has a fascinating universe ripe with potential for cultural clashes, nature vs nurture arguments, quests for redemption, and self-discovery by humans and ponies alike each seeing themselves through the others' eyes. You would never know it by reading pro-pony fics, which take the opportunity to endlessly rant about how much humanity sucks. Or pro-human fics, which spend so much time blasting the pro-pony fics that they forget to tell an actual story. A small handful escape these traps and wind up being very provocative reads - but not many.
Rooting for the Empire: Despite various misanthropic writers trying so desperately to paint the Human Liberation Front as terrorists (and sometimes succeeding), the fact that the deck is so stacked against them and the blatant Moral Myopia of the ponies makes the HLF much easier to sympathize with.
Strawman Has a Point: The primary antagonist group is supposed to be the Human Liberation Front, who believes the ponies are a threat to humanity and must be destroyed. They're treated as unambiguous, totally evil villains, but they're completely right about the first part.
Conversely in the more pro-human fics, the ponies can come off as surprisingly reasonable. Their basic argument is that humans are savage, violent war-mongers who shoot first and ask questions later... except that in the vast majority of the pro-human fics, that is exactly what the humans do.
You are mentally forced to speak in pony-lingo like "everypony".
You almost immediately change your name as well in order to be more like a pony, further discouraging cultural diversity. In A Taste of Grass, one minor character ends up changing her name twice- once to fit her original human occupation of being an entomologist, and then again when she discovers her special talent is actually supposed to be cooking.
You also can't do anything violent, even if it's in self-defense.
Related to the ponification potion is the barrier itself, which wipes away anything that was created by humans in a way that leaves no evidence of their prior existence; which includes the arts, sciences, physical memories, buildings, and human advancements; in other words, the last step of the perfect genocide.
On another front, is Celestia a genuine savior to a dying human race? Or is she a ruthless opportunist taking advantage of a bad situation for her own selfish gains? Or is she a cruel, insane goddess invading and subjugating Earth for her own twisted purposes?
Anvilicious: The messages in her stories are delivered with roughly the grace and subtlety of a train wreck. The plot commonly is set aside for extended passages in order to expound upon the author's beliefs regarding gender, technology, science, the environment, religion, etc. through what are nominally supposed to be the characters' thoughts. Individual stories are never used to convey a single message either; the same worldview is summarized again in its entirety in every single story.
"New Universe Three: The Friendship Virus" is a particularly extreme case. Fans of show are repelled because it has nothing to do with ponies. Conversion Bureau fans are turned off because it is a Conversion Bureau story In-Name-Only. Men would be repulsed at the incrediblymisandric subject matter and the idea of forcibly feminizing men via bioterrorism. Women might be put off by how Chatoyance portrays all women as being nurturing and kind by default. So who or what is this story supposed to appeal to exactly?
Audience-Coloring Adaptation: Many of the elements associated with The Conversion Bureau and its spin-offs such as the misanthropy and the humans having to have their personalities changed are due to Chatoyance's works rather than the original story, which had some of the former but not as blatantly and only the vaguest hint of the latter... for better or worse.
Recombinant 63 seems to be one for the series. After eighteen stories portraying the Earth as a diseased Crapsack World where humans spend joyless and pointless lives subsisting on flavorless synthetic food in decaying slums overrun by violent street gangs and where terrorists carry out mass executions in the streets with impunity, the protagonist of the story is forced to flee her upper-class existence and finds the favelas to be thriving socialist utopias with access to freshly-grown produce, where all lifestyles are celebrated and the inhabitants live in perfect harmony with one another.
Chapter 8, in which the protagonist and the cross-species lesbians sheltering her go shopping in faux-leather fetish wear, the ponies drawing a small cart and being whipped while onlookers cheer in approval, all while the protagonist narrates how her enhanced pony senses allow her to smell their arousal is just a wee bit odd.
Bile Fascination: There are those who read her work just to see how misanthropic they are.
Broken Base: Even more so than the rest of the Conversion Bureau. There are people who love her stories and the universes they depict, and there are those who think that they're a nightmare of bad writing and Unfortunate Implications, and there's very few in between.
Crazy Awesome: New Universe Seven: Mankind Triumphant. Humans steal the statue of Discord, feed it through a rock crusher, coat a nuclear warhead in it, send it through the barrier, and detonate it, destroying all of Equestria and obliterating all of Celestia except for her still screaming head, which is locked away in a magic-proof box. That's pretty badass.
Creator Worship: Blatantly obvious in the comments on her blogs and stories.
Critical Research Failure: Contrary to New Universe Three: The Friendship Virus, men are not responsible for 98% of all violence and rape.
She has stated that her interpretation of Celestia, who is basically the omnipotent god empress of Equestria, is more in line with Lauren Faust's original version of the show, despite Faust herself directly stating that Celestia is not actually a goddess.
Michelson and Morely of The PER: Michelson and Morely - The Speed Of Right are the heroes of the story but they do things like engage in ponification attacks.
The princesses count, too. They're always the heroes even when they're committing genocide. And the ponies themselves, who are painted up as being inherently morally better than humans just because they're ponies.
The bio-terrorists from New Universe Three: The Friendship Virus, who are hailed in-story for bringing about world peace and eliminating crime and violence by releasing a DNA altering virus that turns both men and women into a bunch of Stepford Smilers.
Designated Villain: Humans are depicted as evil in the extreme unless they convert — even if they have done nothing wrong. Those who convert are merely "misguided" beings who are being 'uplifted' into a supposedly better state of living.
On a smaller scale, any character who refuses to convert and calls the ponies out on the genocide they are conducting is written as such. Not only are they totally unsympathetic and beyond any kind of redemption on their own, they must be forced to convert.
Fanon: Chatoyance openly states that her version of Equestria, the Princesses, and the ponies is "more in line with Lauren Faust's original vision" than that of the show and can get quite upset when the show deviates from her fanon. And if the comments about one of her few non-TCB stories, Around the Bend, are anything to go by, this attitude also extends to episodes and setting information written by Faust herself.
Mary Suetopia: The ponies of Equestria live in perfect harmony with their surroundings and with each other, free of vice, prejudice, and anything that the author does not approve of.
Misblamed: Of the "Garbage In, Garbage Out" variety. Chatoyance is often blamed for initiating the virulently misanthropic tone of many TCB works. However, as stated previously, the original story's first chapter was quite misanthropic.
Overshadowed by Controversy: Chatoyance's stories are already very contentious, but three stories in particular stand out: Ten Minutes: Aftermath, a Fix Fic that was interpreted (due to how Chatoyance posted the link to it right on the original author's comments page) as a middle finger to the fans of the original Ten Minutes story; The Reasonably Adamant Down With Celestia Newfoal Society, which has been interpreted as a very caustic Take That!to her critics and critics of the TCB universe in general; and New Universe Three: The Friendship Virus, a Conversion Bureau fic In-Name-Only with overtly misandric messages.
There's also the fact that Chatoyance was also a well-known and hated internet personality before MLP was ever even aired, having been extremely controversial in the transgender scene for reasons which shall not be elaborated here. With TCB being just the latest 'scandal' in a long string of questionable things she's done/said.
Sacred Cow: Her stories are almost revered by her fans. Criticizing them will almost certainly lead to Flame Wars.
Seasonal Rot: Chatoyance accuses the second season of undergoing this. And to an extent, the third season as well.
Straw Dystopia: Earth could definitely qualify, as it essentially is seemingly made of everything that the author does not approve of. Nearly every non-human creature has been driven to extinction, with the few left being unable to be seen by any but the richest. The planet is run by the greedy rich elite who only care about their power. All religions are Corrupt Churches, wallowing in wealth obtained by cheating the poor out of their money. Almost everyone has cancer which can be treated with over-the-counter inhibitors, but only the rich can afford complete remissions. On the other hand, for the first time in history, all humans are fed and watered.
Unacceptable Targets: Criticizing her or her work with her fans around is an invitation to some serious backlash. In fact, in November 2012, she claimed to have temporarily given up writing Conversion Bureau stories due to people criticizing her work, though how much of that was from legitimate complaints against harassment and how much of it was a Wounded Gazelle Gambit was up to individual interpretation. She returned in late December 2012, only to pull a similar stunt around March of 2013. Detractors of her work took her claim that she was "leaving the fandom forever" as yet another cry for attention and had little in the way of surprise when she returned around July of the same year, after placing up a number of long rants on her Fimfiction blog, accusing anyone that didn't like or criticized her stories (even those that gave constructive criticism) of being bullies trying to undermine her.