The Conversion Bureau/YMMV

Flame War: The original and its spinoffs tend to inspire these. Half of the comments decry the series as disturbingly misanthropic, while the other half fanatically defend it as an accurate representation of humanity's flawed nature.
Fridge Brilliance: Celestia is dramatically more powerful and has a different personality than her canon self. If the Gods Need Prayer Badly trope is in effect for the Conversion Bureau universe, this actually makes sense: Celestia multiplied her number of followers several times over in just a couple short years, so she's riding high on an ENORMOUS power boost.
Idiot Ball: An Azure Future, in spades. After an entire story of wanting to remain human and not undergo conversion, the protaganist pulls a complete ideological 180, joins up with a terrorist organization and helps them successfully carpet-bomb a human settlement, then gases a cop whose only mistake was trying to give him a speeding ticket. Making the whole matter worse, the only reason he decided to help the terrorists was so they would convert him in exchange - something that is their entire purpose to do anyway. Not to mention he could've walked into any of a dozen nearby Conversion Bureaus and had the process done legimitately by trained professionals at any time. He receives nothing worse than mild disappointment from Celestia for the whole thing.
Internet Backdraft: Expect the comments section for any of these stories to get ugly, fast.
Love It or Hate It: People have very strong opinions about this story.
Never Live It Down: Blaze acquired an enduring reputation as a absolute misanthrope due to this story.
- The misanthropy laced first chapter is widely mistaken as being emblematic of the fic as a whole.
Straw Man Has a Point: The primary antagonist group is 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.
Tear Jerker: The spinoff fic Last Man Standing makes both the humans and ponies vastly more sympathetic than the original and treats the Purification as a necessary evil. It centers around a man who is about to get killed in said purification because he refuses to get ponified; he has to come to grips with the fact that his species is about to go extinct, and the ponies have to deal with the fact that there's absolutely nothing they can do to save him. He dies triumphantly though, having managed to preserve human history with the aid of Twilight Sparkle.
Unfortunate Implications: By the truckload. Most notably, one race is forcing an entire separate race to convert, giving up all of their history, culture, and identity to conform to the new race's rules and order, or be slaughtered. This is treated as a good thing.

Works by Jennifer Diane Reitz (Chatoyance)

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; the same worldview is summarized again in its entirety in every single story.
Crap Saccharine World: Equestria is a bright world of plenty ruled by benevolent deities and there is no war, hatred or violence. Too bad that its inhabitants are essentially slaves to an insane goddess.
Designated Hero: Michealson 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.
Fanon: JDR 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.
- Comments about her most recent story, Around the Bend, show that this attitude extends to episodes and setting information written by Faust herself.
Fanon Discontinuity: JDR rejects nearly the entirety of the show's second season. She also rejects portions of the first season. In fact, she rejects everything about the show that she dislikes, which has resulted in her re-writing more or less the entirety of the setting, characters and events.
Karma Houdini: The princesses essentially commit genocide and get away with it.
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.