What Could have been

I feel the need to list off these, since they're still sort of mulling around in my head:

Sequel to Love in a Hopeless Place

As part of the fic showed, there were original plans to do a sequel or two.
The original plan was to cycle through two survivor groups: The first consisted of Rainbow, Ditzy, Scootaloo, and a handful of other ponies that managed to stay safe. They would have salvaged the remains of Twilight's balloon (destroyed in an ill-fated attempt to escape), and used it to flee to Canterlot, which was protected via Shining Armor's Shield magic. they would have ran into Gilda, and eventually make it to Canterlot...only to lose Ditzy at the last possible moment.
The Second Group was Rarity, Big Mac, Applebloom, Dinky, and a few others. They would have been forced to go on the ground, and eventually run into Trixie (bunkered down in her carriage) and Rover (dynamited the caves to seal in the infected).
They would have eventually used the armor Rover had, gem carts and Carriage to form a sort of armored carriage and give Mac a suit of armor.

Discordverse

Of Pirates and Parentage
Deleted because I ran into issues writing it, it would have seen Ditzy return to Ponyville to try and reconnect with Dinky.
A rival pirate group, consisting of Vinyl, Raindrops and others, would have noticed and tried to invade Ponyville to capture Ditzy to try and blackmail her pirate crew.
The ponyville defense force (Basically the Elements) would have held them off while Ditzy signaled her own crew, leading to Pirate Captain Rainbow Dash taking her away crew, Doc Sweetheart, Flitter and Cloudchaser and probably a few others, to help retake the town.
It would have hinted at Dizzy's past, as Dizzy would hare redoned her gauntlets, and beat the crap out of Vinyl when she tried to take Dinky hostage.
We would have also met Dizzy's Husband, Bulk, and revealed that Dinky's father is Rainbow Blitz, making her Rainbow's half sister.

A discussion between friends
At some point a new pony would have came to town and taken a job as Mayor Cheerilee's other assistant.
She'd become friendly with Lemon Hearts, since she spent a lot of time at the Library, and the episode's whole framing device was that Lemon Hearts had invited her over for tea:

"Like it?"

'It is...It is a different type."

"I got it from a friend in the Griffon Empire," Lemon Hearts took a sip, "How are you enjoying working with Turner?"

"He is..interesting."

"I suppose that's the polite way of putting it," Lemon Hearts placed her cup down and smiled.
"So tell me, when exactly where you planning on telling us the Truth, Selena? or should I call you Princess Luna?"

The episode would have shown Luna's exploration through the new Equestria, eventually reaching the hermit Kingdom of Equestria. She would have seen what it had become, and Princess Cadance would have revealed that she's also head of the rebel movement to overthrow the kingdom and bring equality. Luna would have returned to Canterlot, and admitted she was wrong, and that she needs to learn more.
Discord would have told her to take a mortal guise and learn.

Thriller Night

Nightmare Night goes bad as Twilight and Trixie unleash the zombie apocalypse on Ponyville.

Luna would have revealed herself, in order to defeat the two, and gain more acceptance.

Modern Major General

A filler of Admiral Bonbon vs Science Pirate Lyra and more.

Bad Moon Rising

A three-parter where Celestia returns and kicks off the second Equestrian War.
Part one would have ended with the Equestrian invasion of the Republic.
Part two would see the Kingdom defeated, Celestia arrives and gets blasted with the Elements.
it would have ended as Celestia reveals she hasn't been fully purified and rips the remnants of Nightmare Moon's power out of Luna, transforming herself into Eclipse, and plunging the elements into eternal sleep.
Part Three would have seen Luna and Turner dreamwalk through each of the element's nightmares: situations where they have to make a sadistic choice over what their element stands for. Big Mac's, for instance, would have held him in the conundrum of who to give that last bit of food to: his family or the starving masses. It would have ended with them fully purifying Celestia, who immediate flees.
Bit of dialogue I had planned out:

"...So we have to go and free them all then?"

"Yes, Time Turner, we must act quickly. I was able to free you, but the other will not be so easy," Luna turned, "Come now."

"...Wait, Princess, why weren't you affected?"

Luna paused.
"Because I have already lived through my nightmares."

Everypony's got some pony to love
The lil' rascals: Applebloom, Dinky, Scootaloo, and Sweetie Belle try to help get Big Macintosh and Rarity together with the Love Poison. Unfortunately, things get screwed up as Rarity spills her drink and the first pony Mac sees is...Thunderlane.
It then gets split between the group trying to cure Big Mac, as Thunderlane flees, and the awkward date between Turner and Luna.

The issue gets solved as Thunderlane runs into his actual marefriend, Mjolna, who's a very husky, vaguely slavic workmare who fights Big Mac to a standstill, eventually knocking him out.

Mashed-up
a counterpart to Magical Mystery Cure, Luna messes up a spell, swapping around the other five's cutie marks...but because it's a retroactive change, it causes a brand new Alternate universe:
Rarity is the ruthless corporate business leader of the Apple Conglamorate.
Thunderlane is a good natured citrus farmer.
Big Macintosh is the nations most wanted desperado.
Dizzy is the Pirate Queen, in the middle of a power struggle with the Griffon Empire
Lemon Hearts is a mad scientist tinkerer ala Doc Brown.

unnamed Equestria Girls counterpart
Would have been Turner and Luna going after Sunset Shimmer, who's been going back and forth stealing valuables.
It's not a High School AU: Turner, Luna, and Thunderlane would both be about 20-something year olds, Rarity and Mac would be in their early 30s, Dizzy and Lemon Hearts would be about 50.

There were no plans to work in the Changelings, at the time.

Golden Gem: Agent of A.R.M.O.R.
Golden Gem and her team: Princess Umbra, Alicorn Mac, Pirate Flitter and Cloudchaser, and Bellona going around the multiverse saving universe and what not.
The first universe would have been them saving a Bad Future Crusaders-esque universe, overthrowing the evil Twilight.
there would have been a chapter where Gem meets her Equestria Girls counterpart and her regular human universe counterpart.

Untitled Turnerdash baby fic
Would have been Dash giving birth and the early days of raising Temporal.

there's probably other things that I've forgotten, but those are the big ones I would have done.