Twilight Sparkle's difficulty in social situations (most clearly seen at the start of season 1), her love of studying and reading, her knowledge of magic, and her Super OCD all point to her being an aspie or a high-functioning autistic. The WMG page and the Princesses section has more speculation.
Since Twilight has the darkest hue of the Mane Six, it's not uncommon for Humanized fanart of her to depict her as Black, Asian, or Indian (mostly following the variouscommonstereotypes). This doubles as a Genius Bonus as well: horses with dark coats in real life actually do have dark skin underneath.
Also interesting, given the pseudo-Greek aspects of Equestria and the ancient Greek Real Life belief that unicorns came from India.
"Lesson Zero" gives more insight into Twilight's personality, specifically her deepest fears: She's absolutely terrified of failure and the thought of not meeting the expectations of others (a trait further solidified by "The Crystal Empire"). Add her general social awkwardness, the fact that she always wanted to throw a slumber party (even though she and her friends are now adults), and even the lyrics of the full version of the theme song ("When I was young I was too busy to make any friends / Such silliness did not seem worth the effort it expends.") her obsession with studying and being a good student seemed to be all she had to validate her own self-worth. Now that she has real friends, she's completely terrified of losing them and reverting back to the lonely filly she once was.
The events of "The Cutie Mark Chronicles" have lead some to speculate that Twilight's obsessive studying and list-making are all about retaining control of her magic. Basically prior to the day of the test she was studying to be like Celestia, after the test she's studying so she never again turns someone she loves into a potted plant.
Twilight's relationship with him also gets much scrutiny. Sometimes she seems to view Spike as a beloved family member, other times as just an employee she can order around. After all, Spike is explicitly a baby dragon who does lots of hard work for nothing but food and a place to live. There's a reason that parody fanworks often outright call Spike a slave.
Where exactly did Princess Celestia get the egg that Spike hatched from? Did she conjure it up with magic, or find it abandoned somewhere? Or did she overpower a dragon mother and steal her soon-to-be child? The fact that "Dragon Quest" gives the set-up to answer this question but never delivers in the end only raises further questions...
Rainbow Dash's tomboyish nature, raspy voice, and rainbow motif have caused some people to come to certain conclusions. Lauren Faust herself has noted that this is rather unfair to all of the jockishly tomboy straight women and feminine lesbian women out there.
Rainbow Dash is often implied to be a Lazy Bum, yet she has also been shown working her rump off when it's important to her (such as constantly practicing her moves) or to Ponyville (she's a team leader during Winter Wrap-Up). Is she lazy, or is she bored by what she sees as trivial duties and consequently slacks off? Given her preternatural skill in tasks she's interested in, such as being the only pony in recorded history to perform a Sonic Rainboom, she might be Brilliant but Lazy.
"Testing Testing 1-2-3" adds a new layer to this by strongly implying that Rainbow Dash has a learning disability.
One YouTube commenter had the idea that Rainbow Dash has Winston Churchill Complex - she equates affection with achievement and assumes that if she isn't the best at what she's doing, her friends won't love/respect her, which would possibly explain her fear of failing/losing and her increasingly erratic behaviour in "Sonic Rainboom" and "The Mysterious Mare Do-Well." This could also explain why she idolises the Wonderbolts as much as she does.
Some people suggest that she and Applejack got the wrong Elements and that she should have gotten Honesty while Applejack should have got Loyalty.
Pinkie Pie being a Fourth Wall Observer with Medium Awareness who ignores it when it suits her is an ACI so widespread most fans assume it's true. Granted she does interrupt the Iris Out on three separate occasions, and many times she appears to look directly at the audience (Word of God says these are coincidences... at least they used to be, though sometimes in seasons two and three these fourth wall references seem to be intentional).
After "Party of One" it became very common for fans to depict Pinkie as judging her self-worth entirely by her parties and how much other ponies enjoy them, which is used to explain why she's so eager to be happy and (literally) bouncy all of the time. Less common is the interpretation that she is outright mentally ill, with manic-depression and schizophrenia the usual suspects.
Another point of evidence to the former theory, in her "Smile" song, Pinkie sings "There's one thing that makes me happy and makes my whole life worthwhile / And that's when I talk to my friends and get them to smile."
Some fans have noticed that Pinkie's abilities (Offscreen Teleportation, obtaining objects from nowhere, ignoring the rules of magic, use of Wrong Context Magic) are very similar to Discord's, leading them to conclude that she is a demi-goddess of chaos like how Discord is a full god of chaos.
Fluttershy's possession of the Smart Ball in "Suited For Success" has led to her exhibiting similar behavior, and that level of knowledge about a number of fields (from writing to gaming to politics), in various fanfics.
Due to an offhand comment in "Over A Barrel", some people think she's obsessed with becoming a tree. (Her disguise in "Hurricane Fluttershy" probably only added fuel to that particular fire.)
Were Fluttershy's actions during "Putting Your Hoof Down" simply her trying to be more assertive, or her letting out her true feelings?
Speaking of "Putting Your Hoof Down", did the entire town of Ponyville just happen to take about twelve levels of jerk-ass or, since this is the only time we've seen Fluttershy interact with them in general, is this how they always treat her? It might explain why she tends to prefer the company of animals.
The episode itself has received this, with some believing it is actually a Whole Episode Flashback to a time before Twilight arrived, since Angel was never that much of a Jerk Ass in earlier episodes and Fluttershy herself isn't that timid in earlier episodes.
Because of season one's finale, Fluttershy has been thought of as more than a little unstable due to her rather terrifying outburst.
Additionally, because of the numerous situations in which Fluttershy kicks extreme amounts of flank (making a dragon cry, staring down a cockatrice, giving belly rubs to Cerberus, counter-trolling the spirit of chaos) it's common to depict her as the scariest pony in Equestria, and that those who know her know to be cautious around her.
In "The Return of Harmony", is Fluttershy really incorruptable pure, or is she just saying whatever (she thinks) Discord doesn't want her to?
In "Sweet and Elite", the behavior of the Mane Cast outside of Rarity lends itself to some speculation. For instance, was Twilight genuinely ignorant that Rarity was ditching her and the rest to hobnob with the Canterlot Elite? Or was she feigning ignorance to help Rarity save face? Or was their immediate act to crash and trash the Garden Party them being spiteful and they were feigning niceness? Or were they just drunk (we don't see Spike, so they might have been serving intoxicating beverages).
Apple Bloom's friendship with Twist. Did Apple Bloom abandon Twist for more popular friends? Did Twist abandon Apple Bloom after getting her cutie mark? Or do they hang out off-screen because Twist can't be a Cutie Mark Crusader?
When playing the fan game Story Of The Blanks, CR says Sweetie Belle is Rarity's daughter instead of sister, jokingly. (A Shout-Out to Gavalanche's fancomics where Rarity is really Sweetie Belle's abusive mother who prefers to be called her sister.)
Scootaloo is the only member of the Cutie Mark Crusaders who has had no familial connections shown or even hinted at, and is rarely seen apart from her two closest friends. Additionally, she's a pegasus unable to fly for anything but short distances, and is rarely seen without her crude wooden scooter. As such, Scootaloo is often depicted as being stuck in an abusive family, or as a homeless orphan.
It's known that pegasi have to learn to fly. So far Scootaloo has not shown any interest in flying. Does she not want to fly, or is she outright incapable of flying? As confirmed in season 4, Scootaloo is unusually old to display no aptitude for flying; Scootaloo being disabled was something thrown around during the series' development, but it may or may not have been abandoned - the ending of the episode in question leaves it ambiguous as to whether she is truly incapable of flight, or merely a very slow learner.
Some humanized versions of Scootaloo have her with a prosthetic limb, due to the aforementioned plans of her originally being disabled and the ambiguity that she may actually be disabled herself.
Another theory gaining some popularity is that Scootaloo is the product of a mixed marriage and for whatever reason-death, divorce, etc.-the Pegasus parent is a missing parent, leaving Scootaloo to be raised by an Earth Pony or Unicorn, neither of which can teach her how to fly. The Cake twins being born to Earth Pony parents has led to an alternate take, where Scootaloo is a "throwback" born to two non-Pegasus parents.
PrincessCelestia's characterization can vary greatly depending on who you ask or what fanfiction or fanart you look at. Canonically she's a wise and loving Big Good, but in the fandom she is very prone to Ron the Death Eater characterizations.
Some see her as a Troll, perhaps as an effect of her immortality and position making her day-to-day life very dull and thus she needs to have fun sometimes. She does demonstrate a more mischievous and fun side sometimes, such as inviting the Mane Six to the Grand Galloping Gala in the hopes they'll liven up the boring tradition for once. While she can still be loving and wise while this way, some fans go for full Jerkass God who toys with her subjects for her own amusement.
There's also the interpretation that she's full evil, ruling a Crapsaccharine World as a vicious tyrant who enforces conformity, segregation and control. These can vary from her being a Knight Templar who sees such control as needed to keep Equestria from falling apart, to Despotism Justifies the Means, focused on keeping her control over the land by any means necessary.
Some fans have noted that devastating, highly important events in Equestrian history are either completely unknown to the general populace (Discord's reign, the disappearance of the Crystal Empire) or only known through inaccurate myths (Nightmare Moon's longest night). They thus speculate that Celestia regularly alters official histories to remove undesirable elements, which in turn has speculations as to whether she does this out of misguided benevolence or a malicious attempt to hide her own mistakes.note One alternative to these alternatives is that she just lets the natural distortion of historical events happen, and everyone usually thinks she's too busy or important to fact check with her. In Nightmare Moon's case, who's going to ask her about the time she banished her own sister and risk reopening old wounds?
Some fans have also noted the rather troubling number of ponies who have feared being banished by the princessnote Twilight Sparkle, Fluttershy, and Rainbow Dash on three separate occasions. Are they just being paranoid, or does Princess Celestia have a history of banishing ponies for arguably minor infractions of the law?
The "Molestia" interpretation is so common it comes with its own sub-categories; from a shiftless layabout who has grown bored of her duties and dodges administration to watch porn, to a very open but harmless nympho with a light BDSM fetish (the most popular, thanks to the infamous Ask Princess Molestia blog), to a serial-rapist and pedophile.
Celestia as a Broken Bird is a less common but still prevalent interpretation. The theory goes that fighting against Discord, forced to banish her sister, and spending a thousand years defending Equestria from frequent threats all alone, while everypony else dies of old age, left her bitter and permanently hiding behind The Queenly Mask.
Speculation about Celestia's relationship with Twilight is rampant, with interpretations ranging from polite but distant professionalism, to a close friendship, to Twilight being Celestia's only friend aside from Luna, to outright romance. A common theme in nearly all of them though is Twilight having (or used to have) a crush on Celestia.
In most of the two-parters, Celestia is put into question. Is she The Chess Master who has thousands of Batman Gambits lined up, can plan someone's life from the day they were born, but can be lopsided when an Outside-Context Villain comes into the picture with a plan of her own or is Celestia a General Failure whose successes are either based around relying on Deus Ex Machinas, the villains holding Idiot Balls or pulling off last-minute resorts in a desperate attempt to gain some victory? Both these interpretations have evidential footing and it all falls in how the viewer sees Celestia, either in a positive or negative light.
Is Nightmare Moon really a Green-Eyed MonsterMad God or was she banished for leading the ponies into an ultimately failed civil war against Celestia's rule? Combined with the aforementioned "Tyrantlestia" interpretation is the theory that Nightmare Moon was the hero and is only the victim of Written by the Winners.
It isn't even clear what Nightmare Moon WAS, given that once the Elements of Harmony were used on her, she reverted to Princess Luna, who is far more mild-mannered. Was she brainwashed by the elements, or was Nightmare Moon some sort of possessing force that Celestia herself could not extricate? The IDW comics seem to indicate that Nightmare Moon was the result of an outside force, given that they possess Rarity and make her their new Nightmare Queen. However, it's not clear if the show treats the comics as canon, though the episode "Princess Twilight Sparkle" involves a magically-induced flashback to the birth of Nightmare Moon, where Luna is seen to be enveloped in an orb of shadowy magic while in the middle of a rant against her sister. She doesn't appear to be the one causing said magic and is in fact thoroughly freaked out, so the "possessed by an outside force" explanation looks far more likely now, though it is sadly not followed up on.
Celestia and Luna being Physical Goddesses is itself an ACI; there are numerous hints for it, most significantly their dominion over celestial bodies, the aspects of nature they represent, and their extensive lifespan, but the actual word god/goddess has never been used in the series. Less common is the interpretation that they are "merely" extremely powerful ponies, or two of the few remaining alicorns after their race was nearly rendered extinct.
With the introduction of "Age Spells" in "Magic Duel", spells that can alter the age of the target but can only be cast by the most powerful of casters, Princess Celestia and Princess Luna's immortality may not even be inherent but the product of repeated self-cast Age Spells (which would also explain Luna's difference in appearance between her first and second appearance).
This is further complicated by the presence of Princess Cadance. Is she also a Physical Goddess? We're told she's the niece of Princess Celestia, but she couldn't be Luna's child since Luna spent the last thousand years in the moon. So who are her parents? Is she also immortal and will outlive Shining Armor? Does she even have a blood relation to the Royal Pony Sisters? (It should be noted that Cadance was originally conceived as a unicorn but made an alicorn because of Executive Meddling.)
Twilight Sparkle and the Crystal Heart Spell expanded on Princess Cadence's backstory and where she came from: It is revealed that Cadence was originally an orphaned pegasus that was adopted by an earth pony village. A Wicked Witch by the name of Prismia attacked the village by draining all their love for each other. Cadence somehow defeated her and was magically transported to the same "interstice" that Twilight went to when she completed Starswirl's unfinished spell. She met Princess Celestia there and was turned into an alicorn, adopted by Celestia, and made a princess herself. Whether this is canon or not is up in the air right now, but this is the closest thing to a backstory she has so far.
Then Twilight became an alicorn, also making her a princess, bringing another whole host of questions. Do all alicorns "earn" their ascension this way? If so, how did the other three do so? Can it be given as some sort of reward or a Enlightenment Superpower? Is Twilight now immortal? And if she is, is this a way to give Celestia some more company for her eternal life?
Is The Great and PowerfulTRRRIXIIEEE a Jerkass, or insecure? Was Ponyville a lousy stop? Did the Mane Cast have the right to interrupt her show and performance with heckling? There's also a very large part of the fanbase that remains adamant that she is just as powerful, if not more powerful than Twilight, despite "Boast Busters" showing that her special talent is in stage performance.
Others have suggested the exact opposite. One fanfic, The Liar, portrays Trixie as a run-of-the-mill con artist. It suggests that Trixie has NO magical ability, that her powers are all based off of the machines she uses in her act (including powdered poison joke to disrupt attempts to show her up), and that her special talent is really the ability to tell the perfect lies. (Fair warning: This fic reads in reverse chronological order)
A common fanon portrayal of Trixie depicts her Miles Gloriosus streak as a mask over a Dark and Troubled Past with a side order of woobie. (It's quite possible you get bonus points for the degree of cruelty with which you kill off the parent who inspired her to start a magic act.)
Others have suggested that Trixie suffers from an Inferiority Superiority Complex; she didn't make it in magic school because she was a bully whose only real talent was using her telekinesis to pick on others compared to other unicorns that can do much more useful magic. Similar to common fan theories about Applebloom's nemesis Diamond Tiara, this theory holds that Trixie is such a showboating Jerk Ass because her talent is nothing special and she's desperate to convince herself and everypony else otherwise.
Perhaps Diamond Tiara's bullying is her lashing out at others because her special talent is merely wearing jewelry, possibly on the issues of Truth in Television beauty pageant attendees.
Similarly, Silver Spoon may be a stereotypical "queen bee" because she's insecure about being rich and useless, hence her cutie mark.
Despite her rhetoric against Blank Flanks, the only ponies Diamond Tiara is ever seen bullying are Applebloom and those who hang around Applebloom. Maybe she's less a generic bully and hates Applebloom specifically (and by extension, those she's hanging around). "Flight To The Finish" seems to support this, as the two switch to bullying Scootaloo about her inability to fly when they realize their "Blank Flank" comments aren't getting to the CMC anymore. (Although they did have a reason for going after them specifically that time - they were worried about the CMC's act being better than theirs and wanted to destroy their confidence so that they would lose.)
Diamond Tiara is usually thought to be a simple Alpha Bitch (although see the Trixie example for one way some people interpret her more sympathetically), her friend Silver Spoon is sometimes suggested to be a much nicer filly who is mean to Apple Bloom because she's imitating her best friend. Silver Spoon is noted to genuinely care about Diamond Tiara's feelings, seeing how she tried to cheer her up at the end of "Call of the Cutie", and was also the very first in the class to applaud Granny Smith's story about how the Apple Family founded Ponyville despite Diamond Tiara refusing to. Although she hasn't had any Pet the Dog moments since then.
Is he the Anthropomorphic Personification of chaos that's just hard-wired to want chaos, just as the ponies are hard-wired to want harmony and peace? If so not only is he unwilling but incapable of maintaining anything resembling a moral compass; even if he could feel empathy for the beings he torments for his own amusement, he wouldn't be able to maintain it long enough for it to make any difference. By this interpretation, he is The Sociopath because he's hard-wired to be incapable of internalizing emotions that could let him live in harmony with others; by his very nature, Discord must consider himself separate from and in conflict with the rest of existence. Keep Calm And Flutter On seems to suggest he can understand and even enjoy friendship, however his selfishness and chaos-mongering tendencies have always prevented him from ever having a real friend.
As of "Keep Calm and Flutter On", has Discord truly reformed? Or is he just pretending to play nice, still intent on screwing with people but keeping his actions within a certain limit so he won't be imprisoned again? In the opening for season 4, he's unconcerned with the havoc his vines are causing, and he refuses to tell the main cast what they are, for no real reason other than his own amusement.
His relationship with Twilight; Is it a platonic/obsessive friendly antagonistic relationship much like Q and Picard? Or is it that Discord has a Foe Ya Y with Twilight? It seems that Twilight is the only one he sees as a Worthy Opponent and constantly teases her like a childish boy does to girls he likes. His friendship with Fluttershy could be a way to get in good with her social circle and start making his moves there. To add ACI on that, is his relationship with Twilight a mirror image of his relationship with Celestia? Could it be now that Twilight is an Alicron, he's projecting his feelings of Celestia onto Twilight?
Were the Windigos evil spirits intentionally causing the ponies suffering and grief, or non-sentient beasts who were merely feeding and their natural way of survival made them a dangerous threat?
The same episode made people claim, as a joke, that Fluttershy was clairvoyant.
Is Queen Chrysalis a bad guy seeking to subjugate an entire nation to make her and her minions stronger, a Jerkass Woobie who is a victim of her upbringing, or a Well-Intentioned Extremist who just wanted to feed her people?
Do the Changelings need to feed on love to survive, or is it merely a luxury that they use to become stronger? Are they innocent non-malicious mooks who can't help that their food source is draining the life out of ponies (often combined with the "their queen is pure evil" interpretation for extra Woobie points), or are they as aware as their queen and just don't care?
Fans are somewhat divided over whether or not they managed to survive their fate at the end of the episode (though in the comic series, they do).
Some people have interpreted King Sombra's animalistic behavior as a sign his defeat and long imprisonment have driven him insane. While he was a nasty person before that, this would explain why he acts so feral and inequine. Celestia outright states he was "turned to shadow" when he was overthrown. The phrase "a shadow of his former self" springs to mind.
Lightning Dust (from "Wonderbolts Academy"): an arrogant, self-absorbed victory hound who only respected Rainbow Dash because she was a Worthy Opponent or an enthusiastic cadet who was told to give her best and went too far unintentionally? Spitfire also could be said to hold some of the blame in Lightning Dust's overzealous attitude as she encouraged her behavior and never stepped in once it started getting out of hand.
Granny Smith. Is her eccentricities just "old people are funny humor" or waaay back in her youth was she the Pinkie Pie of her social circle? The Zap Apple prep stuff she's shown to do in "Family Appreciation Day" support this. Pinkie often knows what she is doing even if it seems strange, and it would explain how Granny discovered things like Zap Apples prefer polka dots; she did Pinkieesque things and kept doing them when they made the jam better. Besides, running off into the most dangerous forest in the world alone at night is not very sensible.
The "Screwball" pony flying around with a propeller hat could be like Pinkie: a pony that would be happy if Discord's reign was permanent ("Eternal chaos comes with chocolate rain!"). Then there's the idea that she was created by him.
When she first appeared there were interpretations that she's a normal pony, possibly a baseball star, who only seemed unusual due to Discor screwing with everything.
Blueblood's behaviour at the Gala has been interpreted by some as him recognizing Rarity's intentions, and was screwing with her because he's met countless other mares with the same vapid dream and he's not willing to play the part.
1) An ordinary pony with the same kind of problems as everypony else who's just clumsy and misunderstood because of her eyes (not that popular, but made moreso by Doctor Whooves and Assistant)
2) An airheaded but well-meaning and perfectly functional klutz (this seems to be the most common interpretation, and the one which most closely matches "The Last Roundup")
3) A kind pony with genuine mental disabilities who speaks in broken and (seemingly) senseless sentences that may or may not make sense in hindsight. This one became less popular after "The Last Roundup" showed her perfectly capable of speaking normally.
4) A complete idiot.
5) A genius - smarter than Twilight - who is assumed to be an idiot due to her eyes and clumsy nature (sometimes also has speech problems).
Is Shining Armor an effective captain? Sure, he's immensely powerful and a useful asset, but that would make him deserving of being a special operative, not a captain of the guard, as captains of the guard are supposed to lead and train their troops. Despite deploying their troops in a state of readiness, having a professionally trained army, and having some warning as the changelings bashed against the shield, the Royal Guard lost the capital in about 10 minutes. There's also the possibility of Nepotism. Perhaps he was promoted to captain by Princess Celestia because of his relationship to Twilight Sparkle or Princess Cadance.
Possibly in response to his general Hatedom, there have been several fan works that portray Flash Sentry as a complete Butt Monkey, unable to get the universe to stop hating him.
Pinkie's sister, Maud Pie, has at least two interpretations to her character: Is her general behavior a sign of Autism, or did she deliberately behave in an asocial manner because she simply didn't want to be friends with Pinkie's friends?
The land of Equestria as a whole might be a less-than utopian autocracy where the unicorns stay in power thanks to their control over magic and learning, and the pony population as a whole oppresses and even enslaves the other hoofed races. The posters in this discussion thread analyze the show and eventually come to the conclusion that Equestria is basically a fascist utopia, rife with rigid caste systems, engineered environments, slavery, class imbalance, all controlled at the beck and call of an all-powerful, godlike being that somehow manages to keep her subjects ignorant of the underlying problems of their society.
Another theory is that Equestria used to be a facist caste system because of the the Hearth's Warming Eve play. It is the only time we see the ponies divided along Earth pony/pegasus/unicorn lines and that is explicitly set in the past, implying that modern Equestria is much more racially balanced. If the unicorns somehow controlled all the learning and knowledge, then why is the most prominent teacher character an Earth pony? Also, if the unicorns oppressed the earth ponies in a 'first and second class citizen' manner, then why is the mayor of Ponyvile an earth pony and the Film Flam Brothers run out of town by angry customers?
Just who exactly is benefiting from the friendship reports that Twilight sends to the Princess? Are they intended solely to help with Twilight's personal growth as she learns more about friendship? Or are they for Princess Celestia as a way to understand the common Ponyvillers and how to interact with them? Or are they for Luna? "Magical Mystery Cure" heavily implies that all of Twilight's training, Friendship Reports included, were to make her ready to become an alicorn.
The entirety of this fanfic relies on this concept intensely, as the narrator analyzes almost every character, action, and event in a radically different way than portrayed in the show. From the goodness of Discord, to the evils of Celestia, and the fact that the Elements of Harmony are supposedly powered by dark magic instead of friendship. But the fic plays this up for laughs.
The nature of the dragons as a species is widely debated. Common interpretations are that wild dragons tend to be Jerkasses and Spike's a Nice Guy because he was raised by ponies, while others suggest that adult dragons are powerful and dangerous when provoked but also intelligent and non-malicious, in which case they are the antagonists because we keep seeing them at their worst; the purple dragon had suffered a personal crisis, the red dragon was unreasonable because it was exhausted and the Mane Six kept interrupting his nap, the green dragon overreacted because he thought Spike wanted to steal all his food, and the teenage dragons were immature idiots that hadn't learned how to behave.
Are the duplicates from the Mirror Pool mindless constructs, reflections of Pinkie Pie's surface personality, or simply innocent children with adult bodies? The tone of the episode changes greatly depending on which interpretation the viewer uses. The problem is with the last clone to get zapped: Fans generally assume that she was the very first clone Pinkie created, who spent considerable time learning about the main characters, and as a result had more emotional range and depth than the clones who were cloned off of her. While the other clones cared very little about being zapped into oblivion, she was clearly terrified.
After the brief fallout between them at the end of "A Canterlot Wedding, part 1", much speculation arose as to whether Twilight's friends, brother, and mentor were sincerely remorseful on how they abandoned her, or whether it was a cover-up. Some people considered the former based on how things are in season 3, but others noted that the only person who apologized was Applejacknote Although they were in a middle of an invasion, and Celestia's form of apology can look broken, they tend to say they were just saving their own flanks.
How much of what Shining Armor said to Twilight was him being brainwashed, and how much of it was what he really meant?
Did Twilight's friends, mentor, and brother really abandon and shun her after her outburst until her vindication, or did they walk away (possibly for only a few minutes) to give everyone time to cool down, only to later be unable to find her? One of Equestria's most talented unicorns couldn't have been kidnapped, especially not in the middle of a secure castle on high alert, so she must have left on her own. Worrisome, but there's no reason to think she's in danger and they can all have a long talk after the wedding.
Was Lord Tirek planning to betray Discord from the start or did he feel betrayed when he learned that Discord was omitting info on Twilight?
Did Discord really join Tirek because he wanted to, or was it all part of his plan to help Twilight find her key? He was savvy enough to lead them to discover the other keys through their journal after all. In all it may seem a bit out of character for him to simply fall for Tirek's plan like that. And he may have omitted Twilight at first for this very reason.
Another possibility is that he was following whatever whim struck him, you know, god of chaos and all.
Was the stained glass window depicting Princess Twilight left by Celestia in a moment of carelessness and haste? Or did the pony master of the Batman Gambit deliberately set up the Twi vs. Tirek conflict, to help her get the final key? It might be stretching it, but she might also have set up Discord against Tirek in a Batman Gambit as well.