WARNING: Because this is a shared universe that could be added to by anypony, whatever is posted here is essentially a Schrödinger's Gun to use be it inside or outside of the cultivated Lunaverse. That being said, anything in here is to be treated as an unmarked spoiler unless explicitly Jossed, and even then is fair game for anyone to write about, so you have been warned.
Altwilight will create a cult bent on restoring the Celestian Timeline.After the planned Crisis Crossover, Twilight will either be completely aware or with suppressed memories of the timeline that was. Without the Mane 6 or Celestia to keep her in check, she makes it her goal to revolutionize the Lunaverse into what she saw in the Celestial Equestria, and uses her formidable command over magic and minds to rapidly gain support.
There will be a fight between Corona and Nightmare Moon at some pointBecause it's cool, and because we all want to know the answer.
Luna!Twi ends up being Corona's Dragon along with Zecora.Who better to show Twily real magic than THE most powerful pony around? It would be a nice dark mirror to canon too.
Alt-Twilight will form her own group of Elements.Rather than commit suicide by going anywhere Corona, Twilight will prove her worth to Luna and her brother by assembling what she believes to be more fitting bearers than the Lunaverse Six. Given that she's kind of naive and a touch touched, her 'perfect' army will in fact be slightly dysfunctional at best owing to her over-reliance on dictionary meanings. As an example, her better version of the Element of Generosity could well be somepony who's only doing it to get a write-off on her taxes and who is otherwise a greedy, selfish jerk.
Fancy Pants and Fleur will have a big fight scene with either Greengrass or Greengrass's thugsFancy Pants has been built up as a secret agent for Luna, possibly head of the spy group the Shadowbolts, and is even called 'Bat-pony' by the writers. Greengrass is the Big Bad of season 1's political arc. Even if it's Trixie that takes the Duke down in the end, Fancy Pants will have a chance to show his stuff by thrashing Greengrass or his minions. And if Fancy is fighting, Luna help the pony who tries to keep Fleur from watching his back.
A famine will hit PonyvilleMaybe it was an accident (Parasprites?) or one of Corona’s plans but in the end Ponyville suffers from a food shortage. The other towns can’t help them because of [insert cheap explanation here], so the town is on it’s own. Of course, AJ sees this as a way to show every pony that only the Apple Trust can deal with such a situation and tries to save the town all on her own. In the end…
Corona will hear a recording of the Symphony for Moon and SunNow that it's finally been played correctly, the other alicorn sister will hear it how it was supposed to sound. And she'll...
Duke Greengrass will be defeated in "Grand Galloping Gala"......and as a result, his co-conspirators will be recruited by Corona in "Summer Sun Celebration". It is mentioned in "When There's Smoke" that she's using that dragon's horde to buy off nobles in the Night Court for her next attack. And with their chief manipulator out of the way and them all under Luna's scrutiny, they'll turn to Corona to insure their continued status.
If there's a Season 2, Discord will be the Big BadAnd like Corona, he'll only be defeated in his first appearance rather than sealed away, allowing him to become main villain of the season's Myth Arc.
Discord with "reform" CoronaDiscord can give ponies insanity and take it away. And what better way to get back at his Arch-Enemy than to make her sane enough to be horrified at the things she has done.
The Lunaverse Six will be slightly more horrified by their Mane-Six world counterparts than the Mane Six will be by their alternate selves.The way things are shaping up, most of the Lunaverse versions of the Mane Six are growing more like the ones we see on TV with each passing day; by the time of the Crisis Crossover, the personality shifts caused by not being element bearers will have pretty much eroded. The same cannot be said of the Celestiaverse versions of the Luna Six. What this means is that when they do meet, Trixie, Cheerilee and the others will be more horrified by what they could have become than Applejack and Rainbow Dash will.
Twilight Sparkle's punishment for the Ursa Minor incident will be a few years of community service in Ponyville.It seems fairly clear that during her time in the Mane Six's world, Luna will have noticed that the best way of keeping Twilight out of trouble is to give her a job suited to her interests. Therefore, she'll sentence her to serve out her time working at the Books and Branches Library.
The evil pony from Crisis on Two Equestrias is an alicorn.Think about it.
If and/or when Celestia comes to her senses, she's going to work behind the scenes to either dismantle the Sun Cult or turn into the local take on the Salvation Army.
The reason the vision Zecora had of Equestria's future ends after the final showdown with Corona is sadly obvious.That's because one of the many things Celestia will be atoning for is luring an innocent, albeit extremely misguided, zebra to a needless death.
Luna cut a deal with Discord.Luna may or may not have been jealous for her sister's attention, but also worried about her being the single thing keeping Equestria out of harms way. So when Discord came to town and enforced his rule of chaos, Luna offered him amnesty and regard in Equestrian court to end his reign of terror on amicable terms and keep her sister out of the line of fire. Discord accepted, then drove Celestia to madness, forcing Luna to seal away her sister to keep her safe from herself, and gained the free passage and private audience with the Princess whenever he feels like it.
Luna might be planning on ennobling Trixie.Not only is Trixie safely out of the way out in Ponyville, her successful performance as Luna's mouthpiece could, as Trixie hopes, end up making the showboating loudmouth a grandstanding irritant with a title.
We will never learn exactly what happened at the Ice Palace.The very amusing story of what it was that Trixie did will never be completely explained. All we'll ever know is that it involved a lot of water damage and caused Twilight to think of Ms Lulamoon as an incompetent fraud.
Applejack is terrified of admitting that the Apple Trust is essentially a license to mint bits.We do know that one of the things that Alt-Applejack has in common with Mane Six-Applejack is a fear of being disgraced. The anger that she demonstrates towards ponies that she tells herself are trying to reduce her family to penury is the result of a comforting lie she tells herself about how the monopoly she and her family enjoy is minutes from collapse. Were she to admit that the family has an iron feed-trough, she'd have to experience the shame of worrying about nothing and making an ugly, belligerent foal of herself in the process. This means that she has to treat Carrot Top as if she's trying to take the food out of her mouth; anything to keep from having to say "Ah was wrong."
Applejack's Aunt Orange and Uncle Resplendent Orange are part of the Night Court.As a filly trying to determine her place in life, she visited them and was exposed to a near-lethal amount of political intrigue. This gave her unwanted insight on just how two-faced, conniving and backstabbing ponies can be, at the cost of a deeply ingrained paranoia.
Fluttershy knows what her father did.At the very least, she suspects he ensured Rainbow Dash to have a steady job in Ponyville so that she can always look after her... whether Dash wanted to or not. She has seriously mixed feelings about this: on the one hoof, it's nice having a good friend around... but what if Dash resents being tied there? What happens if she wants to pursue some other ambition, one that'd involve leaving Ponyville? Sadly, she can't bring herself to say anything about it, too fearful of provoking her father or Dash. Because even if it's not purely friendship that keeps her there, she's happy having her around... and scared of what that might say about her. Does that make her selfish? A horrible pony...? What if finding that out makes Dash resent her?! She can't handle the thought of driving her away...!
Celestia will become a Red Lantern.
Zecora is loyal to Celestia, not Corona.Zecora seems to be a loyal Dragon to Corona, but at the end of the day, Corona hasn't taken over Equestria, not even a little bit. Zecora's main actions have been to summon Corona from Canterlot to the Everfree Forest just in time to get struck by the Elements of Harmony - potentially an attempt to see if the Elements would purify her the way they did for Nightmare Moon in canon - and helping her escape Luna's attempt to imprison her again. Zecora doesn't actually want Corona to rule Equestria, she just wants to keep her alive and free for long enough to bring her back to sanity.
The Lunaverse can be traced back to the original G1 series, G4 being a Pandorican reboot.Due to the mention of Tirek and other call backs from deep within the franchise, the Lunaverse is what became of the world of Megan, the rainbow bridge, and the ponies of yore. The mainline verse is an optimized fork where events and the choosing of the modern Elements of Harmony were gamed to be the golden timeline, where as the Lunaverse evolved more naturally.