Fallout Equestria/WMG

Spike or Twilight is probably Watcher.
He mentions Flutterguy, which only they should know about (excluding the rest of the mane cast who seem unlikely to be him). He also mentions making a study of friendship, something with Twilight was doing in the pre-war days. But since he seems to be referred to exclusively as a he, along with presumably a male voice, it points towards Spike. He's also the only one who would most likely live that long. (That or it's just Fluttershy with some crazy extendo-life support and voice changer, which is crazy, but I'm calling it all the same).
 * As of chapter 20, probably confirmed as Spike.
 * Definitely confirmed as of chapter 21.

The alicorns are clones of Princess Luna
Some scientist found whatever was left of her and attempted to clone her from the badly corrupted DNA he recovered.
 * Might be interesting if a future quest had them destroying the original remains and LittlePip had a crisis of faith upon discovering what they were, especially if they happened to be still alive.
 * As of Chapter 29, they're pretty much confirmed as just ponies who have been dipped in the pony equivalent of FEV. And that neither the alicorns, nor their goddess has any connection whatsoever with Princess Luna, or for that matter, Celestia.
 * You could argue that's not true, the Goddess was a gestalt of Trixie, Gestalt, Mosaic, and Twilight Sparkle. Twilight has a lot of contact with Princess Celestia (and as a Ministry Mare, with Princess Luna after the abdication of the throne by Celestia). Inspiration for the project was based on a lack of alicorns during the war, because the ponies needed a power boost.

The alicorns are Nightmare Moon
She did split into three ponies in the second episode. Maybe the radiation mutated Luna and caused her to revert to her NMM personality, now she works with the slavers as a small army of super-ghouls.
 * Read above as with the clones.

The alicorns are being created from exported slaves
The slaver terminal that Littlepip hacks in chapter 7 talks about someone called Stern, who's been ordering massive amounts of slaves to be shipped to her in Fillydelphia. Stern's representative was an alicorn. The slaver writing the journal even brings up the possibility that she's building an army. It could also explain a few other details in those entries: prospective alicorns probably need to be clean adults, hence Stern's scorn for the idea of foals and why her representative was so angered by the idea of drugging the slaves. Plus, in the same chapter, the alicorn who represents Stern offers Littlepip the chance to join the alicorn hive mind.

On a much more subjective note, in a later chapter, Littlepip is surprised to observe that the alicorns don't have cutie marks. Her surprise at this might be leading up to an in-universe moment of Fridge Horror at what the loss of individuality means to converted ponies. Maybe a character in the story will end up changed or a Fawkes analogue will be introduced.
 * And with Red Eye's recent speech on forsaking cutie marks and individuality...
 * And his speech about ponies being ascended by the new godess, yeah I'm willing to call this one confirmed.
 * Definitely confirmed as of Chapter 29.

Steel Hooves is Applejack
The memory Steel Hooves kept was to remember a lover by, but not in the way Littlepip thought; the Earth Pony couldn't view the memory anyway. Steel Hooves knows a lot about what went on with the Mares of the Ministries, and Littlepip knows that only someone close to the Mares could have as much information as SteelHooves does; she does not suspect exactly how close. The Watcher comments that Steel Hooves sounds like Flutterguy, who was a mare with the voice of a stallion. In Fallout, ghouls' voices change due to the ghoulification process, and the sound of Steel Hooves' voice is filtered through her power armor's sound system, which could easily hide any traces of femininity.
 * Seems far less likely after the memory in Chapter 23
 * Actually, his real name is Applesnack. Ironically enough, he was Applejack's boyfriend.

Twilight Sparkle is The Goddess... And The Watcher knows it.
The Watcher told Littlepip that what was hidden in the cave is the "True heart" of Twilight Sparkle, that the other things Twilight has done aren't what define her. The development of the FEV equivalent would probably fall under the Ministry of Arcane Sciences, making Twilight ultimately in charge.
 * Pinkie Pie's final message to Twilight was rejected by "Maripony Terminal #42"
 * Red Eye has indicated that the Goddess is in the base at Maripony. This puts Twilight at the location where the Goddess would eventually emerge.
 * While Twilight is part of the Goddess, the main conciousness seems to be  Who knew?

Homage is a descendant of Dinky Doo
Okay, all we've got going for that is her grey coat and pro-ghoul sentiments (implying that she's met Ditzy). But you've got to admit it would be sweet.

Littlepip will be forced to upload herself into the Gardens of Equestria maneframe
The last Crusader maneframe we saw slowly killed off an entire Stable "to preserve pony life" and had a failsafe that would have involved the chief technician copying his brain into the machine. It wouldn't be surprising if the project did something like "destroy all mutated organisms". Spike will try to use his own brain, but he'll be killed by Enclave pegasi who want the wasteland purged.
 * . However she does all-but upload herself into the other third maneframe.

Scootaloo is a Braun analogue.
She parked herself in a stable and is running ponies through The Monsters Are Due On Maple Street-like scenarios over and over in the hopes of finding a situation that doesn't result in ponies turning on each other.
 * Seems unlikely considering they found what seems to be her corpse in Chapter 29.

Luna and Celestia have turned into something resembling the Master and are the 'Goddess' that Red Eye talks about.
They were holding each other in the end, and the effects of the 'Pink Cloud' are unknown. They could have merged to become something like the Master. They were also the most powerful Alicorns that we know of, so it is possible they could communicate telepathically over long distances. Red Eye could be 'getting his messages garbled' from his cybernetic implants and such. The talks about Unity, and the similar methods of transformation seem linked aswell.
 * Seems unlikely as Luna is mentioned as remaining in Canterlot while the Goddess operates out of Maripony
 * The Goddess is actually.

Littlepip is somehow related to Applejack.
Applebloom said her family was in Stable Two. Littlepip's mother had apple cider as her cutie mark. "Pip" can refer to an apple seed.
 * Perhaps AJ herself made it into the Stable, and I don't believe menopause has been observed in equines... So maybe Littlepip is descended from Applejack and Applesnack.
 * Then again, the Apple family was rather large.

Fluttershy really did turn into a tree.
It seems like an offhanded joke, but it actually be a clever bit of foreshadowing. Since the story is based off Fallout3, Fluttershy will fill a role similar to Harold, the Tree Man, with Bloomburg being her Herbert. Presumably, Velevet Remedy and Littlepip will have some pretty strong What the Hell, Hero? speeches when they meet her.
 * Seemingly confirmed by the end of Chapter 41.
 * Now.

The Enclave will try to use "Gardens Of Equestria" for their own means.
Remember who the main villains of Fallout3 were. The Pegasus Enclave will take control of the mountain and plan to use the device to restore Equestria, so they can make everyone indebted to them and abuse their newfound power to take over.
 * That or since Fallout: Equestria seems to be even darker than Fallout they'll try to use it to exterminate all mutants (aka, everypony in the wasteland).

Pyrelight is Philemena
Why not? It's been said that most balefire pheonixes are feral birds, but Pyrelight is obviously intelligent. She seems content with being a pet for Velvet Remedy, who may also remind her of her former owner. Or even better, Celestia is alive and sent Pyrelight to monitor and help who may turn out to be the wasteland's savior.
 * Entirely plausible, and as of the end of the story, neither confirmed nor Jossed. Run with it!

Ditzy Doo and Homage will help activate the Gardens of Equestria as the new Bearer of Laughter and Bearer of Honesty
Littlepip tells Spike that she's found two of the ponies that he's looking for. It's very heavily implied (To the point where I'm not even sure this deserves a WMG entry) that these two ponies show the virtues of Laughter and Honesty, respectively. Telling you the truth, no matter how bad it hurts.

Calamity will be the new Bearer of Loyalty
Littlepip describes him as loyal, he's a follower of Rainbow Dash, and he seems to have only abandoned the Enclave because he knew that they weren't doing their duty to the ponies of the Equestrian Wasteland.
 * Jossed by Spike in Chapter 21. It is outright stated they aren't the bearers.
 * However,

Velvet Remedy will be the new Bearer of Kindness
She idolizes Fluttershy, tries to be as kind and diplomatic as possible in early chapters, and as kind and diplomatic as prudent in later chapters.
 * Jossed by Spike in Chapter 21. It is outright stated they aren't the bearers.
 * However,

Littlepip will be the new Bearer of Magic
She doesn't have many spells, but the one she has is very powerful, and in the end, spells aren't what matter. Her greatest advantage is her ability to make friends, even with individuals who have tried to kill her. She's a pony who values friendship and, in Equestria, Friendship is Magic.
 * Jossed by Spike in Chapter 21. It is outright stated they aren't the bearers.
 * Personally, I wouldn't be shocked if a Matrix-style twist was being pulled here. She's not the bearer... yet.
 * Indeed, the introduction to chapter 37 strongly implies that Littlepip will find a virtue. Friendship seems to fit best.
 * As of chapter 44
 * Unless we're going under the assumption that  which has not been stated on way or the other, no, she isn't.

Rarity has put her 'little black book' to use .
In one memory Littlepip observes, Rarity discusses with Applejack the viability of. Applejack talks her out of it due to the immorality and dangers of the idea, and Rarity promises to dispose of the book.
 * I was thinking that given her vanity she would be using the book to transfer her soul into a series of other ponies, maybe with the added touch of residual radiation or black magic degrading each one. And she'd get the idea that a relative of her original body would last longer...
 * As of chapter 37

Rainbow Dash is still alive
There was only one skeleton in the shack, and we saw that her "One Pony Project" involved Rarity developing suspended animation technology...
 * In an earlier chapter (21? I don't remember), she was implied to have died fighting Gilda outside Spike's cave, but there was no skeleton there either.
 * Other points in favor of her being alive: Considering that there are currently two unicorns and two earth ponies (well, one earth pony and one zebra) but only one pegasus, having another flyer join the group would round off the team.  Yes, it's somewhat meta conclusion, but the fact is there is a definite Rainbow Dash shaped gap begging to be filled in the story.
 * As of Chapter 39 it looks like
 * Food for thought here. A recording discovered by  However   It was also mentioned how the Single Pegasus Project could only be activated or cleared through her or a single pony of her choice. This might imply she has been the one powering it all this time, and may be in some kind of suspended animation somewhere in the Wasteland, which was also implied earlier in the story. As her fate is still uncomfirmed this could be a likely scenario.
 * Nope.

The mane characters of Fallout: Equestria realy are the new bearers

 * Spike either can't tell, or knows, but isn't willing to risk ANYONE knowing.

The figurines of the Six are soul jars

 * Think about it; Rarity definitely kept using the black book, and one of the things she'd already been thinking about doing with it is splitting off tiny bits of souls into objects, making them invulnerable and enchantable. There are little statues of each of the old mane cast which are completely undamaged in the middle of the wastes after 200 years, often in very hostile conditions, and when acquired they grant Littlepip qualities that the mare in question exemplified. Pinkie Pie's even seems to talk to her sometimes. She's carrying around bits of the ministry mares' souls, and they're helping her to fix their mistakes.
 * Confirmed,

Littlepip is going to destroy the Gardens of Equestria to prevent the Enclave from twisting it to their ends

 * This is Darker and Edgier, right?

Littlepip, having activated the Gardens of Equestria and cleansed the radiation and taint, will enter the control room of the SPP in order to take control of the weather and the celestial bodies

 * It just seems like that's what chapter 37 is building up to.

Repeated exposure to Taint will turn Littlepip into an alicorn.

 * She's already up to Touched by Taint [2], so she's healed by radiation like the ghouls and alicorns. It could go a lot further, no doubt.
 * Considering that Littlepip's greatest magical ability is levitation. What large object would an alicorn "Raise" that would be Important? Perhaps some kind of large ball of ionized gas in the sky or a large white satellite orbiting the planet.
 * Now that she's hit Touched by Taint [3], she's become something between an alicorn and a unicorn, and is now closer to being an alicorn than being a regular pony.

The reason we haven't had an update in over two weeks
Kkat is trying to figure out how to write Discord into the story.
 * Because we all know he'd take over again if the mane cast and the Princesses were killed.
 * A brief gag is made that perhaps Discord is the one stuffing ammo and supplies in random containers for scavengers to find.

Calamity will enter the Single Pegasus Project

 * He is the only Pegasus on Littlepip's side of this war.

Littlepip will become a stand-in for Celestia

 * Think about it: the Touched By Taint perk has made her pretty much as close to being an Alicorn as she can get without her growing wings. Plus, her last rank in Mighty Telekinesis said, "...you might even be able to move the sun." Therefore, when she's finished dealing with the Enclave and fixing the Wasteland, she'll take on the task of getting the sun back on track.
 * Probably Jossed by chapter 43.
 * Definitely Jossed.

Littlepip's 'Little Pony' (The voices in her head) are the mane 6

 * In Chapter 41 it seems as though there is more than one of them up there...

Princess Celestia is still alive.

 * Unlike Princess Luna, Littlepip Never Found the Body of Princess Celestia.

The new bearers of the Elements of Harmony

 * Laughter = Ditzy Doo, Honesty = Homage, Kindness = Velvet Remedy, Loyalty = Calamity, Magic = Littlepip? That just leaves Generosity.

Littlepip will sacrifice herself activating the GOE

 * Remember, this is largely a rehash of Fallout3, and at the end, the Lone Wanderer dies of mass radiation poisoning activating project purity, even though s/he could have just had someone else die doing it. Littlepip is just the sort of pony to get herself killed so that somepony else won't have to, if it comes to that.
 * That said, there are a lot of references to Fallouts 1, 2, and new vegas (Maripony, The Cathedral, Neighvarro, Canterlot being the Sierra Madre). It's also important to note that people HATED the original ending to Fallout 3, and they released a DLC to retcon it to something else. More likely, Littlepip will wander out into the wastes, like most fallout heroes/heroines do at the end of their games.

Littlepip will become an in-universe Memetic Badass

 * True, DJ-P0N3 helped in that regard, but as the years go by, her exploits will get exagerated to the point where she becomes a mix of Moses, Superman, Chuck Norris, Sam Jackson and Kenshiro
 * Littlepip didn't use S.A.T.S., bullets just hit their mark because they knew better
 * In Zebra Speak, Littlepip means "You Are Already Dead."
 * There is no such thing as Homosexuality, only Stallions who have sworn off mares in honor of Littlepip, and Mares Littlepip allows to fantasize about her.
 * Littlepip was so sexy, she turned DJ-P0N3 into a mare, and then turned him lesbian
 * Littlepip didn't lift objects with her Telekinesis, she pushed the Earth down.
 * Littlepip didn't set off the balefire bomb to kill The Goddess, she set it off to get a tan.
 * When the lands of Equestria are in their most dire need, Littlepip will return and save us all.
 * The Wasteland thought it could kill or corrupt heroes. Then it met Littlepip, who then kicked it in the nuts, then killed it, grilled it and ate it for breakfast. She then did a Decathalon and kicked Enclave and Raider flank off of the energy she got from it.
 * Littlepip thought about adopting a Hellhound pup for a pet, then decided it wouldn't be badass enough.
 * Littlepip knew kung fu, but used guns instead because it made things more interesting.
 * They say that Littlepip hunted down Enclave soldiers and canabals. This is untrue and inconsistent with her personality. 'Hunting' implies a posability of failure. Littlepip goes 'killing.'
 * Littlepip is watching you sex up your marefriend, and she approves whole-heartedly.
 * An Enclave soldier had a clear line of sight to shoot Littlepip, but he was to anonymous for her to even bother killing, so she stared him down instead.
 * Littlepip's friends let her walk into Fillydelphia alone, because they don't care what happens to Fillydelphia.

Red Eye wants to make a second Goddess.
Just to be 100% certain that he doesn't run into the same problems as Trixie, he wants to create a new Goddess to produce female alicorns, one that would be loyal to him, or at least willing to act as an equal partner. Littlepip is currently the prime candidate.
 * Addendum: Red Eye wants to create a second Goddess...and he got the idea from Littlepip. Littlepip said something while convincing him to give her the balefire bomb, and Red Eye started planning.
 * Sort-of correct. Red Eye planned to

Discord messed with Rainbow Dash right before the apocalypse so she'd accidentally sabotage things that would keep the Enclave in check.

 * Dash's last-minute idea to disconnect the SPP maneframe from the controls kept from overriding the Enclave's curtain. Her other last-minute idea to connect Pinkie's box to the Ministry alarms to notify her caused the Enclave to nearly annihilate the entire Wasteland before the  was ready. Er...whoops.

Lauren Faust will make this into a Darker and Edgier MLP spinoff series.
Hey, why not?
 * She would have to get permission from Kkat, Hasbro, and Interplay Entertainment.

Someone will make this into a Fallout 3 Mod.
Please?