What if the CMC were actually trying to make Chrysalis desperate enough to let them go willingly? This makes even more sense given that Sweetie Belle's sister Rarity used this tactic once herself. Sweetie Belle, Apple Bloom, and Scootaloo may have been imitating her.
In Issue #3, it seems odd that it was Rainbow Dash, of all characters, to be the first of the Mane 6 to realize their breaking up was a Changeling trick. However, as the Element of Loyalty, she would have regretted doubting Twilight due to such manipulations back at the wedding worse then the others, and thus try the hardest to learn from it and avoid such mistakes again.
Said regret would also explain why she got so drunk on punch that she needed to be reminded of what happened at said wedding.
The Nightmare Arc (#5-8) is set during Season 3 of the show, when Rarity was Out of Focus, really playing into her fears of being forgotten and meaning she lacked the chances to face her flaws, explaining why she was deemed most susceptible to The Nightmare Forces influence.
Season Four of the show opens with Nightmare Moon destroying The Castle of The Two Sisters, why? In this arc, Nightmare Moon plans to destroy Ponyville, the home of her current vessel, to crush what remained of her personality, likely what she was trying to do last time. The same thing also gives another reason why she was trying to destroy Celestia — in addition to Celestia standing in Nightmare Moon's way, she's Luna's sister and despite Luna's jealousy of Celestia, she still loved her. Killing Luna's sister by her own hooves would crush her spirit far worse than wrecking their castle, no matter what sentimental value it had.
One of the trophies the Luna/Big Mac pair win is "Synchronized Water Polo". Polo - as applied to ponies - would be a rather apt sport (and shown true in issue #11), and horses are actually good swimmers so would take well in the water.
In #11s short, Twilight is said to have played as a high charisma mage in the D&D expy. Seems minor, but this would define what she would become (powerful, great friend and leader) and where others failed (Trixie lacking the means to back up her excessive pride, Sunset Shimmer seeking power without caring what other thought).
Cadance's flyer says her foal-sitting services are cheap. Obviously. As a princess, she doesn't really need extra money, and even if she did, she's just too kind-hearted to charge much anyway.
In the Sunset Shimmer short, she's seen rejecting the invitations of five unicorn mares: Moondancer, Lemon Hearts, Lyra, Minuette, and Twinkleshine. Now, considering that Celestia was trying to groom Sunset in the same way as Twilight Sparkle later, in hopes she would become a Princess, this would have also likely involved her having friends to become the Bearers of the Elements, and from this, there's a strong correlation in these five mares: Moondancer (Fluttershy), Lemon Hearts (Applejack), Lyra (Pinkie Pie), Minuette (Rainbow Dash), and Twinkleshine (Rarity), even with the brief characterization shown in the comic.
Equestria Girls Specials:
Babs Seed's older, human counterpart being a straight-up bully makes sense upon realizing that, due to the age difference between her and the Human Cutie Mark Crusaders, the events of One Bad Apple, where Pony Babs had her Heel Realization, likely didnt happen here.
This would also explain the Human Crusaders' antagonistic actions in the Holiday Special due to their never learning the episode's Aesop. It was around when Human Trixie pointed out their actions were causing as much harm as Sunset Shimmer ever did that they realized their wrongness and confessed to it.
Why wasn't this set before Rainbow Rocks when everyone's treatment of Sunset Shimmer would make more sense? Then it hit me; would they have been willing to hear her out/confess before her redemption?
Interestingly, in Legend of Everfree, it's stated that the three previous movies took place in one and the same school year. That means not only that the Word of God cited above got Jossed, but also that the Anon-a-Miss special can easily fit in between Rainbow Rocks and Friendship Games; and quite credibly so, to boot. What would the students be more willing to believe that the recently reformed ex-bully is being framed or that she was just putting on an act and is now back to her old ways?
Issue #16 implies that Ponyville is unaware that the Elements of Harmony are still present, it makes sense the Mane 6 would not reveal that their best defense against evil is missing, less they invite panic and trouble.
Several from the Reflections Arc (#17-20):
The prototype mirror portal seems to be superior to the Equestria Girls one, (able to access multiple dimensions at any time), so why did Star Swirl bother to create another? It can disguise users as local life (he and Celestia were nearly eaten because the first mirror didnt).
It only opens for three days every thirty moons preventing (or at least curbing) the problems Star Swirl encountered when he discovered he and Celestia were travelling too frequently through the original prototype.
Why was Trixie made an alicorn princess instead of Sunset Shimmer? Since main universe Sunset Shimmer demanded to become an alicorn princess, it would seem more likely that her mirror counterpart would instead be granted the position. That is, until you realize that main universe Sunset Shimmer also fled into the Equestria Girls universe. Assuming that there is also a mirror Equestria Girls universe, mirror Sunset Shimmer probably ended up there before she could be alicornized (maybe due to Mirror Celestia throwing her in there).
The Mirror Universe version of Chrysalis is implied to be far more powerful than the main one, since she's being entrusted to protect parts of the country from Evil Celestia and Luna while her prime countrpart can't even defeat Celestia with her default power level. This makes sense when you realize Chrysalis is a beloved paragon in this world, she's being showered with love 24/7. So where the main universe Chrysalis needs to absorb love to increase her strength to that level, Mirror Chrysalis receives enough love given to her that she's likely constantly at that level or higher.
Season Four of the show (which takes place afterward) opens with Celestia revealing how much Luna's banishment hurt her. Shes learned her lesson that she didnt need to hide her emotional weakness, as trying to do so ultimately cost her in the arc.
Two plot points in Rainbow Rocks:
Twilight having access to Star Swirl's material on inter-dimensional travel would explain how she had the knowledge to build a device to use the EG Mirror at any time, and had said mirror in her possession.
During the movie, Twilight had the same Fatal Flaw as Celestia, being afraid of disappointing those who looked up to them, but by admitting this to Sunset Shimmer, she avoided the consequences Celestia faced. In short, she didn't have to be perfect to live up to, or surpass, the latter's example.
Fluttershy's crush on Mirror Universe Sombra seems to come out of nowhere, unless you remember that she's basically a Disney Princess expy. And who do Disney princesses fall for? The Prince Charming character, which Mirror Sombra is obviously meant to be.
Issue #23 ends with a towering Opal (a result of a growth potion used to help save the town). The comic published just before this, Friends Forever #8, features AJ and Rarity visiting the largest ball of yarn in Equestria, presenting the perfect solution to a giant cat. No idea if the two teams of artists/writers colluded on this facet, but it was noticed by the fandom.
"Siege of the Crystal Empire" Arc:
May also be Fridge Horror, Radiant Hope's Karma Houdini and general overall characterization at first seems to be a case of bad writing. However, there may be a very good in-universe justification for all of it. Hope had been manipulated by masterful liars for centuries. Generally the excuse for being a Turn Coat in the "My Little Pony" verse was of being under a spell (like Discord's Hate Plague), but here it's something much more mundane and realistic. To make matters worse, it wouldn't take much effort on the part of the Umbrum either. One "innocently" phrased comment here and there over a thousand years would be all it would take.
Furthermore, she's not a Karma Houdini after all, if you think about it; she actually got punished in advance of the arc (i.e. — when losing everything due to Sombra's curse, and crossing the Despair Event Horizon) as well as during it (i.e. — when almost dying from Twilight's blast, due to Hope's Stupid Sacrifice for Sombra).
Relatedly, it was Radiant Hope who thwarted the plans of beings of darkness and despair. Twice.
As Cadance explains, Hope could've just asked for help with the Umbrum instead of doing all this subterfuge. But the thing is, Hope already trusted others for help — in "My Little Pony: FIENDship Is Magic" — and it ended badly: Amore's inaction led to Sombra growing fed up and lashing out! In Hope's mind, they just won't give her or the Umbrum a chance until she forces them to see they were wrong!
That may also be why Hope seemed to not care about how others would be affected by her actions. From her perspective, it was the same level of consideration they gave Sombra (it also helps that she thought the Umbrum were good and unlikely to hurt others).
At the end of the Reflections arc, Mirror Universe King Sombra absorbed the evil of Celestia and Luna's mirror counterparts, becoming a feral creature much like his main universe counterpart, sacrificing his relationship with Celestia in the process. This issue balances it by having the Main Universe Sombra purged of his Umbrum abilities and becomes a good pony once again, even resembling his Mirror Counterpart, and reunites with Radiant Hope. A nearby tent with a sign that says "Reflections Custom Mirrors" hangs a very big lampshade on this.
Sombra has often been considered an Expy of Sauron. Come this arc, and we finally see the Equestrian "Morgoth" as well: Rabia.
Issue #39 gave us some good context if we take "Crusaders of the Lost Mark" into consideration. Like Diamond Tiara's line "Who knew ponies without tons of money had problems". This benefits from the context given by Crusaders of the Lost Mark: Diamond's mother puts A LOT of pressure on her due to her status as member of the upper class. Diamond may have honestly felt ponies like Apple Bloom may have had a more carefree life than she did.
In #9, there is a stall selling "Vigors & Plasmids", an obvious Shout-Out to BioShock... which means ADAM exists in Equestria and is perfectly legal and readily available. Let's hope Celestia regulates it more than Ryan did or ponies are more fond of vigors.
The Bookworm from #15-#16, after full persuasion by Twilight not to eat the books, lest he destroys reality, finally got to be the hero of his own book. Then cut to the part where Tirek destroys the whole library, and —given the sheer HSQ amount of destruction— we would cringe at the fate of the bookworm, and all of the characters with it.
In #19, Mirror Celestia says, "If I only had more time with my other self. I could have beaten that spell to her world out of her." Prime!Celestia came back through the mirror badly beaten, but when any of the prime characters are injured, the mirror characters receive the same injuries. Is Mirror!Celestia a masochist?
The parallel injuries only began happening when the Mane Six were fighting Mirror Celestia and Mirror Luna, so it was after Mirror Celestia beat the snot out of Prime Celestia.
In Keep Calm and Flutter On, Fluttershy makes Discord turn good. So with that said, what would happen if Good Discord met Evil Fluttershy? While you could say that he might be able to resist her, it's also just as likely that Evil Fluttershy could just bully and/or trick Discord (by pretending to be his friend) into submission, especially if the anti-mane six join in.
The 2014 Holiday Special showed just how fragile Sunset Shimmer's forgiveness was, with the entire school including the Humane Five turning on her once there was evidence of her wrongdoing without considering why she'd do it, and lingering resentment being the most charitable interpretation of those framing her. If Sunset or the series looked into the implications of that, and asked if it was worth putting up with, or worth trying to be good if everyone was still so quick to condemn her, there would likely be a hard time finding a happy ending.
Also, framing Sunset Shimmer is the human Crusader's plan A. Not talking to Applejack about not spending time with her. No. Plan A is resorting to cyber-bullying. Even after getting the Human Five to break up with her, they continued to frame her for days until they felt enough guilt to confess. For the looks of it, they have issues that the six months of detention they got seem unlikely to address.
Ever darker, it's never clearly established that Sunset's past had anything to do her treatment. Would the school be as quick to turn on someone without her Dark and Troubled Past?
Expanding the universe shows just how much of Equestria is a Crapsaccharine World. Break the law? No problem, the authority won't use magic on you, even when you're hurting her friends, because you're a legal citizen. Nearly drowned the entire populace? You're let off the hook because you were just trying to help your friends. Invade your neighboring country to expand your territory? Well, don't worry. The ruler of said country had so much excitement, it's comparable to when her kingdom nearly got overrun by shape-shifting monsters partly due to her own fault. Oh, and while the authorities might do things to reign in the excesses, they can prove to be just as bad at applying rules in any sort of fair and sane way: Committing fraud and hostage taking? No big deal, you're doing it to stop the aforementioned lawbreaking because they can't just stop them the normal way. Hang around someone that breaks one of the few laws that gives them the authority to use magic on you? You're in for as much punishment as the guy who did. In Equestria, you can almost expect to be a Karma Houdini. That, or one gets a particularlyterrifying, if deserved, fate with little middle ground. One must question Equestrian morality.
"Siege of the Crystal Empire" Arc:
King Sombra's ultimate plan is revealed to spread his conquest of the Crystal Empire to the rest of Equestria, with the griffons and yaks being next. This was around the same time The Cutie Re-Mark showed that he was doing just that in in the timeline he won. With the Umbrum, each of whom could have been as powerful as Sombra was, at his beck and call, no wonder it took all of Equestria militarizing to fight him to a stalemate at best.
After the final battle, Sombra is reformed and all seems well, except Chrysalis has escaped yet again. Now remember in Issue #36, when Sombra and Chrysalis got into a heated argument when Chrysalis spoke out against Sombra's plan to release the Umbrum. With Sombra reformed and likely no longer in possession of Physical God-style Black Magic, he — unless still an abnormally powerful Unicorn like Star Swirl the Bearded, Starlight Glimmer, etc. — and Hope are more vulnerable than ever if Chrysalis decides to take revenge upon him.
Issue #40. A young student is forced to juggle her studies at a prestigious academy with her responsibilities towards the newborn child who suddenly entered her life. Does this sound like a plot of a children's comic book or a teen pregnancy?
Celestia's Not So Different-related Heroic BSoD visibly begins only after she sees Twilight and Luna fall to Accord. Is she contemplating just surrendering so that she can at least be with her sister and surrogate daughter — i.e., Driven to Suicide logic?
Some have speculated that the Elements of Harmony were uncomfortably close to Knight Templar in their methods, what with subjecting victims to millennia-long And I Must Scream and possibly reverting Nightmare Moon to Princess Luna via HeelFace Brainwashing.note The alternative interpretation that Nightmare was a separate entity exorcised from Luna proved unpopular when the comics ran with it. Given their empowering effect on Accord, it may be worth second guessing the Omniscient Morality License they're treated with.