Sorry if my last post came off kind of harsh...I actually do think the "pony genetics" idea is kind of cool, if inaccurate in this particular concept.
I was under the impression Scootaloo either couldn't fly or can't fly well because she's never been shown to, and it seems like by this point, if she could, she would have already, since there have been plenty of opportunities.
From birth to about six months newborns have a natural swimming reflex. After about six months, they lose it. Maybe pegasus ponies have the same thing, but for flying!
This is exactly the same thing I thought of, although I know it's just trying to rationalize what was likely there as an un-thought-out plot device.