Uh oh! New theory incoming! I think I know why Scootaloo can't fly that well!
Ok, remember my old theory when I thought Scoots just lacked feathers because the CMCs kept pulling them off? Well, I made up a newer and better theory that also relates on why we don't see her parents. So as Lauren said, Scoots' parents have high-demanding jobs and never get to spend any time with their daughter, and she feels really lonely because of it. The magic inside her kinda fades away. Did you know that pegasus power is runned by magic?
So basically what I'm saying is, Scootaloo's parents are never around which makes Scootaloo's magic weaken causing Scoots to not fly. She's lacking magic! So perhaps the one thing that will help Scoots finally be able to fly is if she receives the magic she needs to be able to! The answer: her parents! :D
That could be an awesome Scoots episode for the future!