Applejack: Having come back from Manehattan with a way to bring the farm up to a high-class establishment after becoming a lady in Manehattan, the Apple Farm turns into a big factory with a ladylike but menacing Applejack as the Boss. Her cutie mark is an apple-shaped factory building.

Pinkie Pie: Having stayed at the Rock Farm, she too soon takes over, becoming a sort of rival to Applejack's business. Pinkie's insanity comes out as the strange but kind Boss of the Rock Farm. Limestone looks for ponies to work there, and Marble is Pinkie's secretary. Sometimes, she'll 'disguise' herself and go on raids to obtain more rocks (and workers).

Fluttershy: Without the Rainboom to frighten the animals, Fluttershy grew up among them as one of their own. She became a bit of a feral pony and was seen fit by the Rock Farm scout, Limestone, to work there. She's taken up rank there as a guard, and a frightening one at that. Most ponies now call her 'The Guard-dog'. Her cutie mark is a pair of fangs slicing through something.

Rainbow Dash: Having never done the Rainboom, Rainbow Dash became a self-conscious pony who is constantly shadowing somepony else. She went to Ponyville and has now become a worker at the Apple Family Factory, gaining respect from Applejack for her gentle yet firm ways. Her cutie mark is a rainbow stretching between two clouds.

Rarity: Without the Rainboom to break the rock for her, Rarity broke it herself and decided to become a miner. Her cutie mark is a gem-studded pickaxe. After denying Limestone's request for her to work at the rock farm, Rarity formed a little tribe of her own, seeking refuge from the Pie-Apple industrial war.

Twilight Sparkle: After failing her magic exam, Twilight Sparkle was swept into a deep depression and was never seen again. So why has an alicorn version of her suddenly appeared out of nowhere?

Apple Bloom: The little sister of Applejack, raised to take up Applejack's position if Applejack dies. Currently, she is the hard-headed second-in-command of the Apple Factory. But what could the seemingly innocent filly be hiding under that sweet smile?

Sweetie Belle: Rarity's little sister. She lives by herself in a small treehouse outside of the Apple Factory with Scootaloo. Not much is known about her, but she seems to be in Apple Bloom's good graces. However, she seems to be oddly afraid of the Apple filly.

Scootaloo: Like Sweetie Belle, Scootaloo lives in the treehouse and not much is known about her. She seems to want to get to know Rainbow Dash better.

Big Mac: Applejack's brother who was pushed out of the farm-turned-factory by his sister. He now has joined Rarity's little group of rebels.

Granny Smith: She disappeared shortly after Applejack's rise to power.

Diamond Tiara: Ever since her father's business was taken down by the Apple Family, she has become an integral part of Rarity's rebellion. Her cutie mark is still a tiara, and she uses her talent for leadership to help Rarity get her ponies what they need.

Filthy Rich: Having been taken down by Applejack's business, Filthy helps his young daughter and Rarity with the rebellion. He's very self-conscious, but also the main source of advice for the rebels.
What do you think?

4867724
A very good little AU you've developed here.

http://www.fimfiction.net/story/261857/a-world-without-a-rainboom

I have to redo a little of chapter one, but it's on point.

Mostly interesting, but I do have a couple of details..

the Apple Factory and the Rock Farm would NOT be rivals, since they have completely different bussiness.

It's like saying a furniture store is the rival of a car dealership.

Also, Rainbow dash would've flown down to find Fluttershy, she would NOT have simply assumed that she was dead
without actually cheking it personally, and VERY carefully. Remember, they were (and still are, in the canon universe) Best friends.
In fact, before they moved to ponyville, Rainbow was Fluttershys ONLY actual friend, until they met the other elements.
So the "rasied by animals" Fluttershy.. it IS a very interesting idea which I like, but it doesn't make sense unless
she and Dash were never friends.

Other than those details, it sounds like a very interesting idea, and you seem to have a lot of conspiracies and twists,
dark secrets, and other stuff in mind.

Well, the season finale shows what would happen so...