Equestria Girls: Class of '92
Somewhere during the thousand years of Nightmare Moon's banishment, Celestia finds the magic mirror from Equestria Girls. She experiments a bit, and accidentally falls inside--where she emerges, disoriented and scared, as a human. Celestia stumbles around until she is almost hit by a car. She makes eye contact with the driver and stares--behind the wheel is another her.
Pony-Celestia and Human-Celestia ("Cece") return to Cece's apartment. Cece is a college student in the "1990s", and is somewhere in her twenties. She lives alone; she actually used to live with Luna, until she left, suddenly and on bad terms, to study astronomy on the other side of the country. [Alternately: they're still roommates, and excellent friends, which makes Celestia both jealous and sad.]
Cece, unsure of what to do with Celestia, leaves her in apartment while she goes to classes, but not before introducing her to the basics of the microwave, the TV, etc. (Celestia: "But... they don't act like friends..."). That night, they both sit down and have a long talk.
It turns out that Cece is studying something complicated, like engineering or math. However, she doesn't actually like it, and is rather unhappy. Celestia, drawing on her own unhappy experiences, tells her to do what she really wants, and she'll have no regrets. Cece brightens, and reveals that she wants to be a teacher.
[Cece may also give Celestia some advice, though what that would be I have no idea.]
Years later, Cece, now Principal Celestia, brings pony-Twilight into her office. She tells her that she knows she's from another world, and asks her to relay a message back to the other Celestia. She would like her to tell Celestia a little about what she's seen here--and to tell her "Thank You."
AU Celestia x Shining Armor
As in the main fic: on the eve of the Canterlot Wedding, Celestia asks Shining Armor to stand guard outside her office, in an effort to keep her away from not-Cadance. However, not-Cadance, suspecting the gig is up, subtly casts a spell on Celestia. When Shiny and Celestia are alone, Not-Cadance magically manipulates Celestia's own desperate loneliness, along with her own near-total control of Shining Armor, to get the two of them to have sex (with a tasteful "fade to black," of course).
The next morning, Celestia is barely beginning to wake up next to Shiny, when there's a knock at the door. Before she can respond, Twilight, followed by Real Cadance, burst in, eager to go after not-Cadance. However, both of them spot Celestia in bed with Shining, and immediately know what she's done.
Hours later, just as rumors are starting to spread, the Changeling Invasion happens. Without Cadance and Shining's love-bond to stop them, the Changelings are able to take control of the entire city, and Cadance, Celestia, Shining, Twilight, and a few others are barely able to escape. Though Cadance and Shining make up, neither Cadance or Twilight can bring themselves forgive Celestia. Celestia herself realizes that this was Chrysalis's plot the whole time--to drive a wedge between her and her few remaining friends. And, though she feels horrible for everything that has happened, Celestia can never really bring herself to apologize--because, as much as she hates to admit it, she would give anything for another few hours of feeling loved.
And, just as things look like they finally might be on the mend, Celestia realizes she's pregnant.
[This idea, even more than the others, is poorly developed: I have no idea where to take it from here. Maybe Preggo Celestia has to make up with everyone, then take the fight to the Changelings? Maybe Cadance retreats with Shining to the Crystal Empire, establishing an unfriendly and/or hostile kingdom to rival Equestria? Maybe Celestia and her Alicorn daughter(?) are exiled, or leave intentionally?
Though this particular side-story is deader than most of "Equestria," I'd still be interested in hearing any suggestions you might have...]
The Lost Sentry--Suggested by Eruantalon
Shortly after the return of the Crystal Empire, Flash Sentry is feeling lonely and unfulfilled. He goes to the library at Crystal U, where, with the help of a pretty young librarian named Twilight Sparkle, he begins to research to see whether he has any living relatives remaining outside of the Crystal Empire. During their research, Flash begins to notice Twilight, and starts having vague feelings for her; she, however, is either more interested in the challenging research, views him as a customer rather than an individual, or finds him irritating (Perhaps: Flash insists on calling her "Miss." After the third or fourth time, Twilight asks that he call her "Twilight," to which he responds "Of course, Miss Twilight.")
To Flash's surprise, it turns out that, after all the thousand yeasrs of wars, plagues, deaths, disappearances, and "forgot-to-fill-out-a-change-of-address-form"s, he does have a living relative: a distant great-niece, an orphaned young filly named Scootaloo (who, like him, is an orange pegasus).
Filled with dreams of "saving" her from her life on the streets, Flash, with the permission of Princess Cadance, takes a week off work and goes to Ponyville to try and bring Scootaloo back to the Crystal Empire with him. At first, Scootaloo is ecstatic to find that she has family--but the two of them clash over Scootaloo's uncouth, tomboyish behavior and Flash's stuffy, old-fashioned insistence on propriety (and she lives in a very nice foster home, thank you very much).
Things go badly (Perhaps Flash tries to teach her how to fly, not realizing/believing she's legitimately disabled? Perhaps he accidentally breaks her scooter?), but the two of them eventually make up.
On the way back to the Empire, Flash's train makes a stop in Canterlot, where, to his surprise, Princess Celestia is waiting for him. Celestia has heard from Cadance about Flash's mission, and, guessing it was going to go badly, has come with something that will make him feel better: an envelope, which he is to deliver directly to Twilight Sparkle.
Flash returns to the Empire, and, after reporting to Cadance on his apparent failure, goes by Twilight's apartment. On his way, he can feel his heart getting lighter. He realizes, suddenly, that he went to Ponyville for selfish reasons--he was looking to fill his own need for happiness, fulfilment, and companionship, rather than doing good for Scootaloo. However, maybe he didn't have to go that far to find what he was looking for; maybe, there's a chance that Miss Twilight could help in that regard...
It's fairly late at night when Flash knocks on Twilight's door. She opens it reluctantly, and Flash gives her the envelope. Twilight opens it, peers inside, then looks suspiciously up at him--and pulls out two tickets to the Grand Galloping Gala.
[This story would be followed, relatively shortly, by "The Best Night Ever"--which would be set up, rather nicely, by these events]
Flash x Fluttershy
A few months after the funeral, Flash returns to Ponyville by himself. He wanders the town a bit, sorrowfully taking in the sights, before heading to the library. There, he's greeted by Sunshine, who is thriving at her new post: she's redecorated the place, has started some outreach efforts to bring in more visitors, and really hams it up at storytime. She's also taking correspondence courses in the evening, on a wide variety of odd subjects. Maybe she's even dating one of the Apple's sons? (Flash may almost recognize her, but she doesn't remember him at all)
Sunny's cheery disposition rubs off on Flash, and he smiles a little. However, looking around the room at how much she's changed his old home, his melancholy returns. Sunny, sensing the change in his mood, goes quiet as well. She goes upstairs and returns with a cardboard box of personal effects she's found while cleaning out the library--the reason why she asked him to come back. Flash takes them, and sadly leaves.
Flash wanders Ponyville for a while, remembering his life with Twilight. Each new sight depresses him more and more, until he just sits down and puts his face in his hooves. After a few moments, he hears a familiar voice, and looks up to find Fluttershy.
Fluttershy invites him back to her home, and they talk a little. Fluttershy can tell that Flash is hurting, but he, as always, is reluctant to open up, trying to claim that his problems don't matter all that much. Despite his protests, that evening, Flash does not take the train back home, instead opting to stay somewhere in Ponyville (maybe even that bed-and-breakfast from "The Lost Sentry?").
Over the next several days, Fluttershy and Flash spend more and more time together. Flash is still reluctant to open up, but he does begin to share more details about himself: he's gotten a job teaching history at a public school (maybe even the School for Gifted Unicorns?), though the school is too big, competitive, and unfriendly for his tastes. He still has a couple of underage children, who are staying with their sister Aurora and/or their grandparents, the Sparkles. For her part, Fluttershy either never married, or has been widowed for several years; either way, she has no children of her own.
Throughout their various visits, Flash seems on the verge of opening up several times, but battens down the hatches before any real feeling can leak out. However, after several days, Flash says he has a question: as one of Twilight's friends, did she--towards the end--ever say anything about... him?
Before Fluttershy can answer, Flash sobs, then breaks down completely. Fluttershy is startled, but quickly brings him in for a hug. Flash reveals, while blubbering like a little colt, that he blames himself for Twilight's death. He tried to protect her all his life, and, the one time it mattered, he could do nothing to help her. His kids are still struggling, too--they need him to be the pillar of strength he's always been--but, with his own grief, it's too much for him to manage. And, with all these burdens on his soul, he's not sure how he can carry on...
Fluttershy eventually calms him down. Flash, somewhat embarrassed, tells Fluttershy that this is the first the he's cried for Twilight. Fluttershy says that she's gotten very good at helping ponies over the years, and he's not the first pony that's cried on her shoulder before.
Flash goes home, but returns frequently to see Fluttershy. Eventually, they develop into close friends, and, a few years later, get married. Flash is deliriously happy with Fluttershy, though it's a different, and no less meaningful, happiness than what he shared with Twilight. Flash's kids are initially skeptical, but quickly adopt Fluttershy as one of their own.