In Chapter 43, Rainbow Dash notes that the name of the local prankster gang is the "Nobody's Fools", rather than the "Nopony's Fools". In the next chapter, we learn that one of their members technically isn't a pony (Zonk, a zebra/donkey hybrid), and another doesn't act remotely like one (Bowser, adopted and raised by Diamond Dogs).
And a later chapter establishes that they have a griffin among their ranks as well.
The Windy City arc is not (just) an author tract. Rather, it is an elaboration of plot points brought up much earlier, before the hunt started. The Crownbreakers express similar fears as Applejack did about the sweeping changes to come in Equestria, but they are much more violent and much less reasonable. Two of the problems the Royal Sisters seek to solve are the illness and frailty brought on by old age, along with any other problem that could prevent their little ponies from fulfilling their full potential, and the hospital administrators that drive Hospice Care up the wall are one of the reasons they've had little success so far. Mach One encapsulates this to highlight the very important questions that weren't even asked or answered by anyone, Princess or not, at the start of the story; the same ones that none of the main cast have the perspective or experience to even account for.
The ascension spell transluminating all the Mane Six may seem like an inexplicable divergence from canon, but there are certain facts which make it obvious exactly why that happened.
First, RH confirmed in one of the footnotes that he'd slightly changed the wording of the spell. The original implied that it was about fulfilling one pony's destiny, while the altered version more clearly invokes the joint fulfillment of many destinies.
Second, this version of Twilight receives an extensive explanation regarding what the Elements are, how they work, and what can be done with them. She is also much more willing to question tradition and authority than the canon version.
Third, Twilight knew that the version of the spell she received from Celestia is incomplete and non-functional, and would therefore need to be modified.
Therefore, it seems most likely that before ever attempting the ritual, Twilight read over it many times, saw that the phrasing implied the use of others to ascend the caster, and altered the phrasing to something more egalitarian.
A reviewer pointed out the logic in Rarity proving herself to be very skilled at economics. After all, she is generous to the point of bearing that element and then becoming of Alicorn of Generosity herself. And yet she still managed a thriving business selling clothes in a town where clothes were rarely worn with no signs of tight finances, before she could capitalize on the publicity of being an alicorn.
Bold Lion, an expy of Leonardo da Vinci, being responsible for Malfunziona being imprisoned and ending the Medieval Stasis he kept Equestria. He was an inventor, one who had many inventions. And he probably maintained his records daily like his real life counterpart. Meaning he was the best one equipped to notice what was going on and figure out how Malfunziona's powers work (he put his inventions together and could identify just what broke each time) and how to neutralize him using that knowledge.
In chapter 7, the Princesses trick Shining Amour into participating in the ritual to make him an alicorn - in other words, they perform a dangerous and unnecessary medical experiment on an unwilling and unaware subject, something which in Real Life would be very unethical and illegal.
In chapter 46, the Mayor of Windy City is ready to lock up all of the Nobody's Fools (who the readers know are all around Scootaloo's age) when there's the slightest hint that they're involved with the Crownbreakers. Imagining what might have happened if Rainbow's crew hadn't showed up and the same evidence was found is unsettling to say the least. Not helping things is that the Mayor Fussbudget is clearly motivated by his own personal grievances and political greed rather than doing it because it's needed.
In chapter 48, we see that healthcare in Windy City is more focused on counseling rather than curing, even if the patient can and wants to be cured. Earlier, Mach said he had a wing amputated because it grew wrong. Was the amputation really the only choice or was it because of this mindset? The fact that the hospital administrations care more about their philosophy and disregard patient rights and well-being in favor of this philosophy is unnerving.
In chapter 50, the Crownbreakers' plot comes to fruition. They have agents place cloud-solvent bombs over the stadium in such amounts that Mach says they turned the stadium into a pizza while an audience that is roughly half flightless with some of those flightless members being handicapped kids is in attendance. Then, because the clouds aren't rained out properly, the destruction turns them into a supercell. Had the Wonderbolts, Dash, Ajax and the Fools not reacted as they did, Windy City might have seen an Equestrian 9/11 and as it was, Scootaloo and Mach missed dying from free-fall by the skin of their teeth and only because Dash ascended Scootaloo and then Scootaloo ascended Mach. The Crownbreakers agents Mach catches and interrogates think this is all justified for the purpose of, quote, “Knocking one of the fake princesses off her high and mighty throne—”; they're willing to murder hundreds of innocents because they don't think Alicorns should rule.
And there's the fact that Dash is an Alicorn and virtually her entire retinue are Pegasi, both of which can fly. None of the ostensible targets of this terror strike could be harmed by it unless they were injured before then, meaning the Crownbreakers are either totally blinded by hatred or they're willing to kill anyone in their way to their goal.
Mach's speech in Chapter 45 argues that all three tribes only tolerate each other, and all communities are set up in a way to subtly exclude the other two races. Specifically, cloud cities, which are completely inaccessible deathtraps to non-pegasi. There "used to" be a custom of literally bumping off physically-disabled pegasi foals off the cloud city's "ground" - and they still don't have any guardrails. Remember Fluttershy's backstory? That's why nopony tried to help her when she fell.
In chapter 25, a husband and his pregnant (and about to give birth) wife are being menaced by a kappa, with only two cucumbers between themnote Like in the source Japanese mythology, kappas will spare you if you give them a cucumber with your name carved into it. This particular kappa is planning on waiting for the wife to give birth and eat whoever's name wasn't carved., and the father prepares to perform a Heroic Sacrifice for his wife and unborn child. Later, when the mother-to-be finally gives birth, we learn she was with triplets... meaning that, if Sweetie Belle's search party hadn't found them, both the father and at least one child would still have been eaten.
RC's hangs a few lampshades on the Cutie Mark Crusaders gaining their reputations as troublemakers and wreckers in fanfiction, by pointing out at the Fridge Logic that they haven't actually done ANYTHING in the official materials that would explain why they are viewed that way by the fandom in chapter 52. Explained in his own words below (in response to someone calling the Ponyvilleans over-dramatic and saying the CMC ascending is tame compared to Pinkie).
Kind of the point. The CMC have kind of become a fanfiction trope for "walking natural disaster." Yet I thought it over... what disasters have they actually unleashed? Twittermites, Ursa Majors, barn collapses, vampire fruit bats/fruitbat vamponies, dragon attacks, the Smarty Pants incident, go cart race crashes, buffalo range wars, Wintersplosions—- all the actual major disasters that have hit Ponyville, Canterlot, Appleoosa, etc. in canon have been the fault of the ADULTS, more often the Mane Six or their friends. The most actual damage the CMC ever actually caused themselves was the talent show collapse and the wreck of their parade float— and in both cases they were the only victims. So how did the CMC get a reputation in fanon as cute little whirlwinds of mayhem and destruction? In the story I'm assuming that a great deal of rumor, gossip and coincidence are involved. In many cases, the CMC's older sisters/honorary sister have been right in the middle of the catastrophe. So three loud, rambunctious fillies would more often than not be nearby as well... Hear a loud crash, see three fillies in the vicinity, toss in some highly selective and biased collective memory and away you go. Gossip is often cruel and always unfair.... and this is one of the CMC's grievances: the same Nosy Neighbors and Useless Adults who couldn't seem to notice when the three were being bullied, have noticed every little mistake the girls have ever made and gossiped them into being walking disaster areas.
