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There's more stuff I wanted to post for the Exileverse before posting this, but I decided to get this one out of the way since it's one of the more complete concepts.

While Flash does live in Ponyville and formerly Canterlot, his hometown is Cloudsdale. He is the firstborn child in their family, but he has to share his birthday with his twin sister, Lightning Dust. It's important to know that since Flash took Rainbow Dash's place as bearer of the Element of Loyalty, Lightning takes Rainbow's place as a regular pony. Lightning Dust is the lead weather pony and Wonderbolt hopeful in Ponyville. As for Scootaloo, she's Flash and Lightning's younger sister. While she does love her big brother, she completely idolizes her big sister to the point where it can be called hero worship. Scoots is the reason the family lives in Ponyville. Not once did she fly when she was a little foal. It took one incident of her nearly falling from Cloudsdale for them to realize that it was very likely she was flightless, so they moved to Ponyville. Scootaloo was still a baby when they made that decision, so doesn't know that she might be flightless and the family doesn't want her to know until they know for sure. They found documented cases where pegasus foals didn't fly for the very first time until they were old enough to earn their cutie marks, so there's still a chance that she can fly. However, because they're so focused on finding out all they can about her possible medical condition, Scootaloo doesn't get a lot of attention from her parents and it's perceived as a lack of support. It's why she turns to her siblings rather than her parents whenever she has a problem. To her, Flash and Lightning are the only members of her family that seem to care. It's a point of view/lack of communcation thing. Her parents care a great deal about her, but she thinks they don't care at all because they're putting all their effort into solving the flight problem she may or may not have and doesn't know about.

Anyway, since Lightning takes Rainbow's place in all aspects but as the Bearer of Loyalty, the Sonic Rainboom event changes. For one thing, Lightning got her cutie mark prior to the event. Secondly, rather than having a rainbow ring spread across the sky, the sonic boom Lightning causes when she races the bullies that were picking on Fluttershy is magically charged with electricity. Instead of a Sonic Rainboom, it's a Sonic Shockboom. This causes a slightly different series of events that leads to the Exileverse main six getting their cutie marks. Fluttershy and Twilight Sparkle earn theirs the same way, but Pinkie Pie's story changes a bit. Rather than having the rainbow be what makes her smile, the static charge that makes her mane puff up does. She starts a playfight with Maud before they both bust out laughing. That's what gives Pinkie the idea to plan her very first party.

I still have to work on Big McIntosh and Royal Pin's cutie mark stories, but I can tell you Flash's. He was watching the race when she pulled off her shockboom. The sight caused ponies to panic since it was the first instance of a pegasus creating an electrically charged sonic boom. During the chaos, Flash saved a filly from being trampled. He found that protecting ponies was what he was meant to do, so his cutie mark appeared.

As for Wonderbolts Academy, Rainbow plays the role of the reckless cadet since Lightning is playing Rainbow's part. Nothing really changes since it's just Rainbow and Lightning switching places.

Parental Glideance was a challenge, but I figured it out. Scootaloo wanted to write her hero report on her sister, but Lightning suggested that she write about Spitfire instead. So, Spitfire takes Rainbow's place in that episode.