I've long toyed with the idea of rewriting MLP (like say, giving the town more of a reason to dislike Trixie, more with Zecora, etc.). One troubling aspect is the CMC's families. Apple Bloom is an orphan, but she has such a big family you'd never know it (wonder what pain she hides deep inside?) The real troubling points are Scootaloo and Sweetie Belle. Sweetie Belle's parents apparently dropped her off with Rarity and didn't look back and Scootaloo gets tossed aside to so many different caretakers that it's canonically given her low self-esteem. (This show got dark in its later seasons.)

Could you make Sweetie Rarity's daughter and Scootaloo Fluttershy's daughter? You'd need to invent spouses for them, others could look after them when they're away and honestly, a lot of pieces start fitting together. Both Fluttershy and Scootaloo have anxiety issues and are weak flyers. Rarity basically is Sweetie's primary caretaker. This way, the CMC actually have proper families. I'm thinking about doing a story about a Mane 6 and CMC camping trip which goes wrong.

Here's an excerpt-

"The thunder boomed outside and Fluttershy shivered, suddenly pulling Scootaloo into a tight hug. "Shh, it's okay, Scootaloo, Mama's here, it's okay..."

Scootaloo leaned into the affection, even if she looked confused. "Mama, I'm alright."

Fluttershy continued shivering even as the thunder lit up the rocky walls of the cave. Dash laid a wing on Fluttershy's back. "Yeah, Scoots, everything's going to be alright." She shot a look at Twilight. "Twi. Get us out of here."

Twilight shook her head. "I can't, not in this weather!"

"Can't you teleport us home?"

Twilight groaned. "I can't teleport that far!"

Dash sighed. The wild storm wasn't letting up. Electricity crackled in the air. Something powerful and...wrong."

Hmm. Seems interesting.

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Could you make Sweetie Rarity's daughter and Scootaloo Fluttershy's daughter? You'd need to invent spouses for them, others could look after them when they're away and honestly, a lot of pieces start fitting together. Both Fluttershy and Scootaloo have anxiety issues and are weak flyers. Rarity basically is Sweetie's primary caretaker.

Rarity as Sweetie's daughter is an idea that has been around for some time. Though, she would have most likely been a daughter raised as a sister because Rarity was too young to care for here. That's a pretty common conclusion for the idea too. I could link you to some stories that feature the concept.

Aside from a few stories centering around adoption, I don't think I've seen Scootaloo as Fluttershy's daughter. I think the dynamic between them would be interesting, but during the pilot Fluttershy is strongly selectively mute. This would likely inhibit her ability to form a relationship long enough to produce a child and negatively impacts her ability to care for herself. A young child would not be a good addition to her household unless Fluttershy showed the abilities she has later in the series.

I think you might have to reconsider for Fluttershy and Scootaloo. However, I do remember Scootaloo being the younger sister of Cheerilee in one of G3's incarnations. That could work, and you could always tweak it so they're just relatives of some kind instead of sisters.

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The concept could work for fluttershy and scootaloo being mother and daughter as fluttershy seems only to act the way she did in episode one to people she has never met or people who have startled her.

I would love to see this concept come to life.