Friendship Is Witchcraft/WMG

Fluttershy has a secret crush on Pinkie Pie.
Her Establishing Character Moment sees her singing "Hellfire" -- something which suits her role. However, the lyrics specifically involve the singer's obsession with a gypsy... and what does everyone keep calling Pinkie?
 * Adding more fuel to the hellfire, Fluttershy apparently told Apple Bloom that Pinkie has "the voluminous hair of a temptress". Is she speaking from personal experience?

Pinkie Pie's family were gypsies.
In the extended version of "Pinkie's Brew", her parents get a verse: "Pinkie, if you're hearing this, it means we're dead and gone / Please don't bake a portal, just accept it and move on." This is how she was able to find the recipe in the first place, as well as why others keep accusing her of being an evil enchantress: her parents were well-known gypsies. (Of course, they likely weren't evil or anything; like their daughter, they were likely beacons of sanity in Ponyville. But thanks to the ponies' Fantastic Racism, they were distrusted and ignored, and after their deaths, Pinkie got shunted into the orphanage because nobody wanted a 'gypsy daughter' bewitching them.) Zecora helps her because she knew her parents.

Robots really do have souls.
Sweetie Belle seems a bit too contemplative and thoughtful, especially about life and death, to be a soulless automaton.
 * Robots don't have souls, Cyborgs do. Sweetie Belle is an experimental Cyborg soldier, Rarity's war crime? Selling children for experimental war projects, even her sister.
 * Or she was in the chariot crash from six years ago. Her parents died, but she managed to survive and was rebuilt.
 * Robots don't have souls. They just have programs to help them emulate pony behaviour.
 * How do we know that robots not having souls isn't just propaganda?
 * You are a robot sympathizer! ROBOT POLICE! ROBOT POLICE!!
 * It is possible that robots don't have a soul, but may gain one depending on their interactions with real ponies, and after getting a soul, they act far more emotional that a real pony would because their bodies aren't prepared to host a soul, also possible that due to owning a soul, robots like Sweetie Belle would just go emo over finding out they are robots, instead of going on a killing rampage.

The parents of the Mane 6 will come back to life, and then be killed as the 9 are saved.
In episode five, Rarity's parents come back to life, but then the sound of a crashing carriage can be heard after they leave. Odds are, the cast will have to kill Fluttershy's dad (again), and the same with any other parents that return.

The spell will save nine, but will be the reason Pinkie Pie's parents are dead.
Because malevolence is hilarious!
 * "They say a kitch-in time saves nine / But I'm just saving two" will prove darkly prophetic: Nine will be brought Back from the Dead, but only two will survive.

Sweetie Belle is not a robot. Rarity is.
Sweetie Belle just has an odd accent and a vision problem. Rarity is, as Sweetie Belle accused, a combat robot who has trouble expressing human emotions.

Trixie, Gilda, and the other Antagonists will be neutral to heroic, but get screwed by the cast anyways.
We've already touched upon Unsympathetic Comedy Protagonist (Twilight is a raving narcissist who forces her friends to play along with her fixations and framed Princess Molestia to try and get her title, Rainbow Dash is a shallow moron, Applejack is a remorseless war criminal, Rarity uses overseas slave labor, Fluttershy is almost pure evil, and Pinkie, while more sympathetic due to her emotional baggage, still abuses Spike and is implied to have plucked out a young colt's eye to make her brew), we might as well go the other way with the antagonists.
 * Trixie will be giving a perfectly normal performance, but when the Mane Cast heckle her, she deals with them vaudeville style. Unfortunately, this inspires them to trick Snips and Snails (by threatening Spike) to go out alone, into a dangerous forest, to retrieve an Ursa Minor, in a deliberate attempt to murder her.
 * Alternatively, Trixie fought in the war alongside Applejack and Rarity, who did something heroic (fended off a massive bear attack) as opposed to war crimes or deserting. She starts off more or less well-adjusted and works as a traveling performer, but it turned out she was captured and tortured by the bears later and now suffers from bear-induced PTSD, meaning she can't fend off the Ursa.
 * Gilda on the other hand, recognizes Fluttershy as the Antichrist that she is, and how the town is completely insane (her other negative traits will be edited down or plays up Pinkie's near-stalkerish tendencies during the episode). She wigs out because she really was being deliberately targeted.
 * She might also be angry at Pinkie for messing up the space-time continuum.
 * Or, building on Rarity's parents, the dragon, and Granny Smith's relation to the Main Six, Gilda was brought back from the dead and is attempting to selflessly repair the timeline.
 * "Damn it Dash! Your pranks are not funny! How do you think I died the last time?!"
 * Dash, of course, will be mortified that she has gained a backstory and thus character depth.
 * The Diamond Dogs will be members of a Saintly Church who want to gather gems so that they can defeat the Smooze. However, they make the mistake of kidnapping Rarity, which brings the wrath of the cult on their heads. At the end, Fluttershy will bury them alive
 * Their attempt to kidnap Rarity will stem from a wish to reform her. It fails, hard.
 * Blueblood will screw with Rarity because he realizes she's just trying to use him for his looks, money, power, and prestige.
 * Flim and Flam actually do offer a reasonable deal but quickly realize the Apple Family are terrible businessponies and try to take it over for the good of the farm. Applejack sabotages their machine.
 * Alternatively, they're from the Equestrian equivalent of the ATF and are investigating rumors the Apples are weaponizing their apples for a strike against the government. Their contempt for Applejack comes from witnessing her crimes during The War.

Rather than Mind Rape, Discord will try to make the girls have Heel Realizations.
And his chaotic magic will be funneled towards Lampshading the already bizzaro nature of the FiW world.

Sweetie Belle is a cyborg from a failed military project.
She shows signs of being thinking and caring, more than simple emulation of emotions can provide. She also has great power, powerful unicorn magic and cybernetic enhancements can cause a very disastrous combination, unfortunately, she was too caring and they had to leave her with her sister Rarity.

The "Secret of my Excess" dub will explain why the Mane Six hate Spike, along with Equestria's hatred for dragons
Either that, or a complete Who's Laughing Now? episode.

The War was against the Livestock Races.
The Sheep are political prisoners, and Applejack's stampede that flattened the school was meant to crash them into a building to splatter them.

Pinkie first met at least one of the others during her time travel escapades.
And that's why everyone's so convinced she's a gypsy at the start of the series. At least one of them remembers meeting her as a filly and hearing her mention her gyspy magic.
 * If "Lunar Slander" is any indication, Pinkie Pie didn't physically go back in time. How all of those people  came back has yet to be explained... but A Gypsy Did It, so maybe we shouldn't dwell on it.

Smooze is a benevolent, if chaotic, being.
However, he was sealed many centuries ago by his enemies, who turned Equestria in the terrible place it is, now he is using deception as a way to get himself unsealed and save Equestria, Fluttershy herself is aware of this, but keep on it because despite the fact she really is evil, she doesn't want her friends to suffer more than they already do.

Rainbow Dash actually has depths...
...But is incredibly ashamed of this for her own reasons. She keeps the facade of being extremely dumb and single-minded to help hide it, but she actually is an extremely intellectual pony.
 * Evidence for this: She needs glasses! Fictional idiots almost never need glasses, but fictional smart people almost always do.

Derpy Hooves's role;

 * A Slenderman-esque creature
 * Like Pinkie, the Only Sane Man

Spike is a robot.

 * He does go on a destructive rampage in Secret of my Excess...

Robots don't have souls...
But neither do ponies. At least, not in a form that can be detected by pony-technology. The scanners at the sisterly anti-robot and free-labor-for-the-Apple-family competition detect biological signs, not souls; this is why cyborgs supposedly have souls, and not that they have the soul from the living pony they still are or (somehow) the dead pony they once were. Smooze may help or hinder this theory, or may be completely irrelevant; he may accept robot sacrifices despite their supposed soullessness compared to living ponies, he may have a preference for meat-ponies and thus accept only living ponies and cyborgs, or really any other reaction. Unless he says something of the matter, though (or tells Fluttershy), any reaction he has could point towards the no-souls, pony-but-not-robot-souls, or (heretical) pony-and-robot-souls.

Equestria, despite being an eternally persistent diarchy, does have a President...
But unbeknownst to Apple Bloom, the position of "President" has something to do with apples.

Apple Bloom will plan to overthrow the royal family and institute a democracy in Equestria.
Given that Apple Bloom is one of the few mostly-decent characters in FiW, this might actually not be twisted into something dark and horrible before someone else gets a hold of the idea, but it probably won't get off the ground before the end of the events chronicled by the series.
 * So far royalty's been relatively sympathetic; Celestia is just doing her job and avoiding Twilight's fanfics like the plague, and Molestia/Luna just wants to have friends. Except... Luna gave her title to Twilight. I think Apple Bloom may end up getting some unexpected aid in her plot to overthrow a princess.

Fluttershy's dad wasn't as abusive as she led the rest of the Mane Six to believe.
He was very neglectful and far from a stellar father, but when Fluttershy finally confronts him, she only mentions him destroying her stuffed animals, missing her softball games and not being proud enough of her drawings to put them on the fridge, and he only admits to throwing her velveteen rabbit into a fire... but there are no mentions of all the horrors that Fluttershy was talking about earlier involving the robotic wolves and the ants or anything even remotely similar.

Which would mean that Fluttershy lied to her friends' faces... something she has done before -- remember her "innocent friendship bonfires" from earlier in the episode?


 * This Troper's interpretation is that everything Fluttershy said he did was true From a Certain Point of View, such that the robot wolves = plushies, and the ants = . . . I'm not sure about the ants, tbh.
 * How do African ants survive in frozen tundra?

Trixie will be Molestia's de-alicorned form.
In anticipation of giving her princesshood to Twilight, Molestia will take the form of a unicorn. But not just any unicorn, mind -- but Twilight's replacement in Ponyville! After all, if she's going to be in Canterlot with Celestia, they're going to need a token 'Socially Awkward Fanfilly Unicorn', won't they...?

Sweetie Belle will be the last pony Pinkie's Brew saves.
There will be nine ponies saved by the brew. Sweetie Belle has no soul. Connection?

The "Dragon Quest" dub will be about Spike's attempt to leave Ponyville.
Since he is hated by everypony, he will try to rejoin his kind during the dragon migration. This time, things will go well until Twilight catch him up and force him back to Ponyville.

Cyborgs are pony robots.
During the war, ponies built robotic soldiers called "cyborgs", where as the enemy planted cybernetic spies into pony society called "robots", which are programmed to blend in until activated. The bit about souls is propaganda (they have the exact same number of souls), while the bit about telling a robot spy that she is a robot is horribly real (as their defensive mechanism is to kill everyone who might know, then forget it ever happened).
 * Sweetie Belle is a cyborg, made from a corpse (the real Sweetie Belle?) provided by Applejack. She isn't in school, because she's been this age for the past ten years.
 * While everyone knows Sweetie Belle is a cyborg (it's kinda obvious), Scootaloo is secretly a spy robot (it stands to reason spy robots would be better at blending in than combat models).

Luna/Molestia has Asperger's.
She's shown several symptoms: poor people skills, low self esteem, trouble understanding social situations (she thought the residents of Ponyville didn't like her because she was scary, when it was actually because they thought she was a clingy dork)...

Sweetie Belle will die tragically
It has already been established that robots are hated and destroyed upon discovery. The series has already made a reference to Do Androids Dream of Electric Sheep? Now all show can use the following line of dialogue:

"Sweetie Belle:"

If they actually do this, everyone will cry like babies.

Sweetie Belle knows she's a robot and has somehow managed to curb her urges to go on destructive rampages.
Sometimes she slips up. "When small things get kicked around, they just might destroy the town", for example.

Pinkie's portals or Fluttershy's copycat portal will cause a massive dimensional disruption...
causing a crossover with The My Little Pony the Mentally Advanced Series that will be too awesome for words.

"When small things get kicked around they just might destroy the town" is a Foreshadowing
Hey, let's kick that baby dragon! I'm sure he won't grow into Godzilla and destroy our town with all the townsfolk.

The Putting Your Hoof Down dub will have Fluttershy's Villainous Breakdown
Particularly in light of canon Fluttershy's "The Reason You Suck" Speech towards Pinkie Pie and Rarity; in this show Pinkie is a gypsy that Fluttershy may be involved in a one sided Foe Yay with and Rarity is Fluttershy's right hoof mare. Whatever causes this will not be good.

The ninth and final one to be brought back by Pinkie's portals will be Lord Smooze.
Being from a previous generation of the show, it's decidedly from the past. Pinkie is unknowingly bringing about its resurrection.