Twilight Sparkle is a direct descendent of both the original Twilight and Princess Sparkle of the Princess Ponies.In my opinion she is descended from G1 Twilight on her mother's side and Princess Sparkle on her father's side.
Tirac will be resurrected and will free Discord from his prison, or vice versa, and they'll team up.Celestia told her General that she didn't want to be disturbed from her meeting with Megan unless that scenario happened. How is that not Tempting Fate Foreshadowing?
Chrysalis and the changelings will appear and be revealed to be connected to Rosedust and the Flutterponies.Cadance and Shining Armor have shown up and are getting married, so the author is obviously incorporating the events of "A Canterlot Wedding" in this timeline. That implies that the changelings exist too; given the nature of the Canon Welding in this story, it's hard to imagine that the author won't come up with a comparison/explanation for these two insect-like pony races.
The prophecy is true.Namely, this prophecy: "'The First shall become the Last, and when the Mag'ne returns she shall lead old and new against the Corruption.'" Now, what is "the corruption"? I have several guesses. First, there's there's my strongest possibility that the corruption is another way to say The Smooze. Second, is the idea that there is some ultimate evil that has corrupted hundreds, and will turn out to be the Bigger Bad of both generations. Third, perhaps it's a metaphorical corruption, meaning that with her return, the corruption of the hearts of ponies will be addressed. (Kinda like how they freed Morning Glory from her own mind)
Pinkie Pie is a direct descendant of Surprise.In "Giggle at the Ghosties" Pinkie states that her Granny Pie sang her that song ("But Granny Pie said that wasn't the way/To deal with fears at all…She said: 'Pinkie, you gotta stand up tall/Learn to face your fears/You'll see that they can't hurt you/Just laugh to make them disappear.' Ha! Ha! Ha!") In one of the flashbacks Megan and Celestia sing a different version of the song and credit it to Surprise ("It's like that song Surprise likes to sing. You gotta stand up and face your fears..." "Laugh and they'll just disappear! Hah, hah, hah!").
Tirac turned Queen Majesty into ChrysalisThe flashback to her defeat at his hands ends with her being consumed by the Rainbow of Darkness. And since we know what that thing does to ponies, it'd be fair to say it didn't kill her, but worse.
My Little Pony Tales also happened at some point.Perhaps a century (more or less) after Megan, Danny, and Molly leave Ponyland for good. The Ponyville in Tales may or may not be the same one in FiM, which was founded 999 years after Megan's last visit in the fanfic's timeline. Somehow and some reason, only Earth ponies are living there, and magic may have been forbidden for a brief period of time.
Beast Wars will happen in the far future (and had happen in the past).Or at least a version of it, since Beast Wars is a pseudo-sequel to the G1 cartoon.
Inhumanoids also happened in this universe.After all, it is another Hasbro cartoon.
Same for C.O.P.S.
The rest of the Mane Six are descendants of the following G1!Ponies...Posey = Fluttershy
Firefly = Rainbow Dash - Firefly married Bloodwing of the Sky Clans, who founded Cloudsdale.
Sparkler = Rarity
The "ancient castle of the royal ponies" was once Dream Castle.Once Celestia and Luna became of age, they made Dream Castle their palace to rule for a time.
Megan's return would inspire a new age, and bring back other creatures.The Flutterponies already came out of hiding. Soon, many other good creatures who were the ponies' allies in the G1 cartoon would re-establish relations to the ponies.
TCB!Celestia will see Omnicorn Megan's memories of Dream ValleyDuring the final bout between the two, Celestia will pin Megan down and try to use a spell that let her see and destroy her memories, making her easier to control. However, memories of Megan first meeting of Firefly, saving Dream Valley from beings like Tirec, help found RB!Equestria, her siblings and her caring for RB!Celestia and RB!Luna during their fillyhood, and Danny's accident from saving Luna, will cause her views on Humanity to be shaken.
In the side story where the CMC + Dinky, Sparkler, and Megan's kids find the TARDIS and use it to find the Brig and Sarah Jane...They will also stumble upon Susan Foreman, AKA the Doctors Granddaughter. He will be plenty surprised to not only see very old friends, but also a family member he thought was long dead. Of course, there will be awkwardness when Susan realizes Dinky and Sparkler are her aunts.
Corona will either appear or be mentioned.To which RB!Celestia will sigh and say, "Oh great, another one."
Applejack's hat once belonged to Megan.In chapter 12, Applejack said "wears a hat like the one I got on now", meaning Megan was wearing a cowboy hat on her first two visits. She may have often wears a cowboy hat on her days in Dream Valley and Paradise Estate. She probably gave one to the original Applejack as a token of friendship, and has been passed down from mother to daughter all named Applejack.
Princess Platinum, Commander Hurricane, and Chancellor Puddinghead will be thawed out at some point.It's been mentioned a couple of times that while frozen, they're still alive, and in a recent blog post, the author did suggest that they might still have a role to play.
Twilight Sparkle is the true heir of Queen Majesty.In addition to being a descendant of the original Twilight and maybe Princess Sparkle, Twilight Sparkle must be descendent of Queen Majesty from her father's side. Or the original Twilight herself must be Queen Majesty's daughter. Majesty was "killed" by Tirek 20 years before the G1 cartoon, and original Twilight must have been sent hiding for protection. Her royal blood must have been kept secret from her and her pony friends in Dream Valley. Princess Sparkle must be referring to Majesty when she told Twilight Sparkle that she'd make her proud. This may contribute to her coronation.
Tirac is responsible for the greatest threats to ever face My Little PonyUpon his Resurrection, his body seems to be composed of a smooze like material. He gained power by creating Nightmare Moon. For all we know, he might have been the one to push Discord into his reign of terror. Thus, the first was also the mastermind, and all the great villains of MLP owe him for pushing them to their schemes.
Discord was another reason (if not THE reason) the humans fled.Knowing what humans are like, they are easily vulnerable to Discord's powers.
The Covenant of Primus foretold the events in United We Stand.Hence the Autobots' involvement.
Jormun the Red is Garble's father.