I feel that although to me it doesn't matter if Scootaloo flies or not(at least to me), that she might end up flying. I feel that it would be nice as well as a good moral in some senses, but in other senses a bad moral for kids watching. If maybe someone had some disability watched the show might think that if they worked hard enough they can overcome a disability, even though for some they might not be able.
As for her character, some might say it would make her a more interesting character, but I feel she would be the same whether or not she could fly. I believe that's the story the show is selling, and I quite agree.