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 Threat of Satanic Commonism, the heroes meet with the head "breast"note Presumably "priest" of Moscow.
In The Evil Gods II, our heroes go to "Washing Dick," and get some boobs from witches.
In The Titans Strike Back, we hear it's a co-story with Attack of the Spank.
Anvilicious: Disagree with the author about anything? DIE. The stories aren't at all subtle about this message.
Ass Pull: The author having to tell us in parenthesis that God told Jerry about The Mole midscene in The Evil Gods I.
The retconning of Michael's death at the end of Battle with the Witches.
When their weapons and prayers fail to defeat Lola, Draco prays for God (never mind that Lola had the ability to make that impossible) to turn his sword into a holy vacuum cleaner, which sucks her up and kills her.
Audience-Alienating Premise: The violent religious fanatics who go around killing people and forcefully converting others are supposed to be the heroes. Needless to say, this series doesn't have a lot of non-ironic fans.
Some of the errors are from the author not bothering to read or watch the source materials; for instance, in The Evil Gods I, it's said that Zeus was Percy Jackson's father, rather than Poseidon. In The Prayer Ponies, Rainbow Dash is presented as male, Cutie Marks are always called "the marks on their butts," and Celestia's name is misspelled in at least two separate ways.
Evil Gods II has some Artistic License with US Government: when a president dies (and then comes back and quickly thrown in jail for rigging the election and being Kenyan), the candidate who ran against him in the last election (John McCain) becomes president rather than the vice president getting promoted.
St. George was apparently a demon. Despite being a saint. It's somewhat more understandable, though, if you consider that he's the patron saint of England, which the author seems to consider an evil country for, among other reasons, Henry VIII cutting ties with the Roman Catholic Church and for being host to Hogwarts.
This isn't helped by Hogwarts technically being in Scotland.
Designated Hero: Our "heroes" are self-righteous, racist, homophobic, misogynistic mass-murderers who made Stalin look sympathetic in universe. Even moreso, they are never seen doing anything positive let alone anything heroic. We never see them feeding the poor, healing the sick, or even stopping to Pet the Dog. They get rid of the "villains," and make everyone convert to Christianity, but the Satanists were actually better people than the Prayer Warriors were, and the conversions are almost all coerced thanks to our heroes policy of killing those who refuse.
Designated Villain: Most of the villains are this, since their "crimes" are often things many people would consider harmless, or simply not choosing to follow the Prayer Warriors' murderous ideology. One interesting example is how Percy Jackson does nothing evil while on the side of the villains, but one of his first acts after converting is to stone Tyson to death for refusing to convert. It's easier to list the exceptions, such as Jupiter, rather than the straight examples.
Esoteric Happy Ending: Satan is defeated, but the United State is now an oppressive theocracy (and in the later installments, England, Ireland and other countries seem to be following suit), Harry Potter has been killed while Voldemort is still on the loose, and a very unpopular Tsar has been restored to the throne, messing up history. Um...yay?
I Liked It Better When It Sucked: The chapters written by Ebony are less preachy, less poorly spelled, better-written and much less disturbing, and consequentially much less fun to read than the chapters written by Thomas. On the other hand, there are gems such as Socrates being referred to as a Roman god, and in the one chapter Noah proofread, Michael struggling to suppress his feelings of attraction to Ginny.
Informed Wrongness: The narration has to tell us just how wrong everything the Satanists do is, thanks to all the Offstage Villainy. Often, it refuses to even specify what sort of "satanic" or "wrong" things the people the Prayer Warriors kill are doing just before their deaths.
Jerkass Woobie: Grover keeps coming back from the dead and getting killed off in many brutal ways. It's almost enough to forget that he's also one of the Prayer Warriors, especially considering he doesn't accomplish that much for them.
Jerry crosses it by having his wife executed for adultery, first by being thrown off a tower, then stoned to death, then beheaded. It didn't stick, but it shows how far he is willing to go to punish sinners.
Michael crosses it by carrying out Jerry's sentence on Mary.
Percy Jackson crosses it by stoning his half-brother Tyson to death for not converting. Ironically, this is worse than anything he did as a villain. And if that didn't do it, he later kills Ebony because she was raped.
Ebony crosses it by killing Harry, then killing Ron for finding his body.
Rachael crosses it by not only killing Idiosy for hacking, but, after she has escaped from his mansion, burning it down and killing all his guards and wives, which is completely unnecessary.
Jason crosses it by putting napalm down Socrates' throat, then after proving that he's not a god, leaving him to have a slow death by burning alive.
Draco, for all his wearing leather pants, so to speak, crosses it by leading a mob with the intention of killing the entire British Royal Family, "men womenchildren and all". He succeeds in killing the Queen, and plans on hunting the rest down after they escape.
Arguably, the act that makes Dumbledore stop being a Designated Villain, at least for the moment, is having Noah executed by being stoned to death because he prayed to God and Satan. Notice that the Prayer Warriors approve of this.
John Lennon crosses it by nailing a group of Christians to corpses and sets them on fire.
In-Universe, several villains are considered to have crossed this by doing things that would come off to some people as completely harmless (Venus kissing another woman), or Pet the Dog moments (Stalin deciding to allow freedom of religion).
The fact that the Prayer Warriors repeatedly point out that they don't bury the enemy's dead. One has to imagine all those bodies, laying around rotting and getting eaten by scavengers.
Some of the death scenes.
Virtually any time someone is stoned to death, especially if you're familiar with how it works in Real Life, as it's a long and painful death.
Chiron is killed and eaten by the residents of Camp Half-Blood.
"Idiot" and "Benjamin" are impaled and set on fire, and cut to pieces and fed to a dog, respectively.
Ginny is blown to pieces by an explosion.
Grover's first death in Threat of Satanic Commonism; both his legs get broken and he gets disemboweled by a spear.
Nightmare Fuel: Religious extremists taking over a country by force in modern times can be pretty disturbing, especially considering the extremists' very narrow definition of the "right religion," and what they do to people who don't follow it to the letter.
Ron the Death Eater: Almost all of the canon characters from their respective universes, both heroes and villains, are warped into Straw Satanists. And yes, this includes Ron Weasley himself.
Surprisingly Improved Sequel: The parts of The Evil Gods II in which Ebony was writing. While it's still preachy and has a touch of sexism in the beginning, it's not an Author Filibuster like the previous three installments. The characters act more like human beings instead of mouthpieces, the dialogue is not robotic, and the heroes don't curb stomp the first bad guy they see. In other words, if Thomas stayed out of it, it would have been a regular fanfic.
They Wasted a Perfectly Good Character: Voldemort, who not only was more in-character than most of the others (although that isn't saying much), was also set up as an enemy to both Hogwarts and the Prayer Warriors. His involvement as a third faction could have made the story more interesting.
So would a story about Hogwarts being destroyed by a group of heavily-armed Muggles who have found out about the wizarding world and want to Burn the Witch!.
Even going with the story that exists, Michael's infiltration into Hogwarts might have been more interesting if he found himself forced to reconsider his beliefs, and possibly become what he was pretending to be. Instead, he simply apologizes to God every time he's forced to do something un-Christian, and purposely fails when he can.
Or a bunch of McCarthyist Americans armed with modern weapons who go back in time to the Russian Revolution and try to prevent the Romanovs from being driven out.
Hell, even the actual premise of the fic has promise! A group of very religious christians clashing with other worlds that obviously conflict their views. Written by a smart and open minded writer, this could have been a very interesting look at both the fictional universe they traveled to and also Christianity itself brining up topics of faith, reliability, and such. But of course, that's not what we got at all.