So this was gonna be all like some story about RD sending a scootaloo who can never fly to talk to fluttershy about how to enjoy a flightless-ish life but then I failed and you know I'm a tool so I'm still uploading it
The darker one is that Cloudsdale was attacked by a dragon while Fluttershy was in her youth and Scootaloo was just a foal. Their parents were eaten, and they got separated in the chaos and adopted separately.
The lighter is that nopony in Cloudsdale knew that Fluttershy survived, and so Scootaloo's parents moved down to the ground (Fillydelphia?) to raise their remaining weak-winged daughter in relative safety. They only moved to Ponyville a couple of months before the fateful Summer Sun Celebration.