Ok, let's explain the situation again because you clearly some pieces are missing:
1)Raven immune to propaganda and why is she the only one treated as Evil:
Both of your statements are false within the story! Raven is not immune to propaganda. Questioning the system doesn't mean you absolutely know it's wrong! Raven spent a whole month (Legacy Day is at the end of September,almost a month after the first day of school) thinking that maybe he had to sign for the sake of his friends, and the decision to rip his belly was made on the spur of the moment.The entire next book sees Raven having to deal with the consequences of this action because even though she now knows that no one goes poof, the equivalent of God in their world has collapsed and people are in crisis.
Furthermore, it is absolutely not true that the other Villains are not treated badly: Lizzie is deeply excluded from every social circle, Ginger is constantly put under scrutiny because"he could poison us and eat us", nobody likes Faybelle and they are friends with her only out of fear
2) Why other Villains embrace being evil: This is false! Lizzie, Kitty, and Faybelle, when they have a POV, clearly express that they exaggerate their evilness because "it's their story." But their private lives are profoundly different. Lizzie is a good girl inside but acts angry because she think s it's what her mother would do, Kitty is in a mischievous role but when she put her friends in danger she regretted it, and Faybelle as a child was much sweeter and it is after years of plagiarism from her mother that she became a mean girl.
3) The Roomates Issues: I honestly don't understand what your problem is with the idea of Maddie and Kitty being roommates, since it's thematically consistent (and they even grew up together).I mean, it's one of the best pairings on the show.
Justine and Ramona were thrown together because they were introduced late in the show and two free-form characters were needed (Had they been introduced earlier they probably would have had more suitable roommates). Yes, thematically they're pretty meh, but they don't destroy any of the show's foundations.
4) Faybelle and Lizzie's friendships:
The Duchess and Faybelle dolls were released around the same time, so since they are the two mean girls at school, the two are best friends in the diaries. It's true, if we look at the reality of the show and the books, Duchess's best friend is not Faybelle, it's Sparrow! But Sparrow doll never came out so a replacement was needed (idem for Faybelle: Her best friend in the books is clearly Ginger, but their storyline was cut from the show.) This is not a plot hole though because this information does not actually impact/is inconsistent with the canon in any way.
If you're asking why the Wonderlandians get along with Lizzie, I guess you haven't actually seen the show/read the books: They grew up together!!! Kitty and Lizzie even live under the same guardian.They are long-time friend. Also, they are from Wonderland, where all the characters except Alice are morally gray. It makes sense that they're friends. Also, again: Just because they live in a theocracy doesn't mean everyone is like Apple!
5) The Evil Queen Has a Life After the Fairy Tale + The Invasion of Wonderland: THAT'S THE POINT! Fairy Tale is a big set up to give divine legitimacy to those in power, that is, the various princesses like Snow White.
Furthermore, The prison thing was only implemented after the Evil Queen messed up. Before, she just had the hot shoes/exile punishment (depending on which version of Snow White you're reading).And that's because the bad guys still have to stay alive because they're part of their world's economy. Because as in the real world, a political enemy has been created that serves to maintain the status
And no, NO ONE ALLOWED THE EVIL QUEEN TO INVADE WONDERLAND - That's exactly why she's a subversive! The idea was that she should remain obedient in her castle because "that's the tradition" respecting the punishment, but she didn't do it. AND THIS IS BECAUSE DESTINY DOESN'T REALLY EXIST, at least not the way Grimm and the Royals want it; that's the point
6) Why the Dark Fairy doesn't do the same thing: Ok, officer you haven't read the books because that's exactly what happens - The dark fairy was supposed to invade other kingdoms, but Raven's mother beat her to it; so much so that now Raven's Storybook reports the invasion of the Beauty Kingdom as a point in the Queen family's history,instead of the Thorns
And yes, Faybelle's mother is an abusive mother! She's described as a narcissist! The difference is that Faybelle prefers to believe her mother's delusions and tries to please her rather than rebel,Because unlike Raven she doesn't have a good second parent to put her on the right path
And then excuse me, why would they chase away the Queen of Hearts? Wonderland is her land, and her subjects love her and her husband. She's unpleasant to Alice, but Alice does nothing to depose her. That's her rightful throne, and that's it! Ditto with the Cheshire Cat: He's a duchess's pet cat, what on earth would they do to him? Sell him to the pound????
7) Why they are still alive: Because once again, fairy tales are a system of social legitimacy!! It's like saying, "Why are you staying alive after you've had children? You've achieved your goal in life!
Baba Yaga isn't a villain in Russian fairy tales (that's the Wizard Koshei), she's more like an ambiguous fairy godmother. It makes sense that Grimm would want such an important figure as Vice Principal.
Rumpelstiltskin doesn't die in his fairy tale, he just goes to hell. And even if he did die in the Grimm story, that's not canon in the world of EAH where bad guys can survive for legacy purpouse.
8) Why Only Raven Has The Good King: BECAUSE HE'S HER FUCKING BIOLOGICAL FATHER. He raised her, because he's her father. The other villain children we know are Faybelle, Ramona, Ginger, and Lizzie. Faybelle and Ginger don't have a father because they are magical creatures (they could be magic created, their mothers could have killed their fathers etc. There are many possible ways), Ramona is just faking evil for not cast suspects on her and Badwolf and Lizzie SHE HAS A GOOD FATHER, AND IN FACT SHE'S NOT REALLY EVIL
Lizzie says several times that she feigns anger to appear like her mother, but in reality she is more docile than her. And in fact, the King of Hearts is described as a magnanimous and funny person, both by Lewis Carol and Shannon Hale.
9) Ashlynn's Father: In all versions of Cinderella, the stepsisters are already adults or at least of marriageable age when they arrive at Ella's house. So King Ella doesn't raise them at all (and also dies shortly thereafter). Furthermore, neither Charlotte nor Prudence are particularly evil in the books, they only want to marry the prince because they know it would help their status (EAH is a deeply classist world,the social climbe is important for commoners)
10) Snow White is the most important: The writers chose Snow White because it is the fairy tale that practically everyone in the real world knows. And yes, it has nothing to do with the villain (or they would have chosen Sleeping Beauty, since everyone remembers the evil fairy), but with the power of the White family. That's the point.
11) Swan Lake: Yes, the story could have happened in 9 months (gestation time) instead of two days because even though EAH's fairy tales are more faithful to the Grimm counterpart than the Disney ones, there is still that something called a NARRATIVE PACT, which implies that in their world some things are different from our version for the sake of the narrative. There is nothing strange in the fact that in their universe the Swan Lake lasts 9 months instead of 2 days, Goldilocks is 18 years old instead of 10, etc. etc. Also because real life fairy tales have numerous versions and are not fixed.
While in Shannon Hale's original trilogy the implications were that Odette was dead and Siegfried had started a new life with Odile (and in fact Duchess is desperately looking for a prince probably to fill this other void as well). Later it was retconned to the swan to make things less dark. But it remains that it is a dark fate - Duchess is destined to lose herself and the love of her life, just like her mother did.
12) The Candy Witch: This is false, the implications of punishment are there anyway! The Breadhouse family is socially isolated and can't do anything. The beats are mistreated. Badwolf has special permission because he's usefull, but otherwise would be in jail. Furthermore, once again, the Villains are part of their world's economy, they can't definitively eliminate them. This isn't Descendants!!!
13) The Woolf-Hood romance: Okay, you really haven't read the books! It literally says that in previous years the school was segregated into classes based on social exclusion. And if it's true that being all in the same institution obviously creates class solidarity, it was still taken for granted that Red would never get close to Badwolf because there are centuries of "Red Hood should not intersct with the Bad Wolf".
14) Apple and Raven friendship: Yes, Apple's initial friendship with Raven is deliberately written to be a friendship of convenience. Apple repeatedly thinks Raven is evil, but she also believes that since the fairy tale of Snow White has A happy ending isn't an insurmountable evil. Apple is deliberately stupid and tone deaf, because she's a privileged piece of shit who doesn't understand why Raven is hurt by the sistem
15) The Huntlynn: This is proof you don't understand the classist nature of the show. Ashlynn can't date Hunter BECAUSE HE'S POOR! Daring dates princesses, so no one has any problems. Ever After society hates the working class, because at the end of the day they're pawns for the royals.In the books, Sparrow is even placed in the class of villains because in their world stealing from the rich is a crime, even if for the just cause of helping the less fortunate. (of which he himself is a part).
Except for Rosabella and Darling, all the rebels are people of working-class backgrounds who are left behind by the system because they are either poor (Hunter, Sparrow, Cerise, Cedar, Maddie), or Bad (Raven) or both (Ginger)
These are not petty motivations, they are very right motivations on their part.