Do you remember all the times Scootalo appeared without her family? I have been thinking, and i got to the pont where she may be a relative to Fluttershy:

  • If you look carefully, the color schemes of both Scootalo and Fluttershy are similar, but it is more darker for Scootalo. 
  • Scootalo may be running away from Fluttershy, thinking that she is not as awesome as Rainbow Dash is. 

Now to say it a bit more detailed. While Fluttershys coat is yellow, Scootalos coat is orange, which are very similar colours if you think of it. Same goes for the mane and tail colour. They muist have some connection or relativness

As we all know, Scootalo is a very big fan of Rainbow Dash, and wishes to be and is under Rainbow Dashs wing. But we also know that she hates girly things, while Fluttershy is kind of girly. So Scootalo may have the fear that her the only things she could do there is play with the animals and some other girly stuff. Which results in Scootalo being away from her (Though she went to Fluttershys cottage in the sleepover)

Buit hey, this is just my own theory, what do you think of it?