I think Fluttershy and Scootaloo were originally planned to be related in some way.

1. The coloration is similar (orange and purple to Fluttershy's yellow and pink.) Both are weak flyers. In fact, neither could fly as foals.

2. Both are prone to panic attacks. Scootaloo's refusal to admit she was scared on the camping trip is reminiscent of Fluttershy doing the same in Dragonshy.

3. This is circumstantial, but their first interaction is strangely sweet and hints at familiarity. In Stare Master, Fluttershy suggests a lullaby to the CMC and Scootaloo is the first to agree to one in a very enthusiastic tone of voice. During the lullaby, her eye line is straight on Scootaloo who is smiling back. (Also Fluttershy wasn't a bad foalsitter in that episode. Getting three probable second graders-if not younger-off to bed with minimum fuss is not an easy feat!)

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Sisters
OR
Fluttershy is Scootaloo's mother

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