These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Also, and especially, we get an alternative interpretation of Fanon Scootaloo when we get the real story. Her quite normal existence of course turns the outlandish stories Twilight's been given so far on their heads, of course, but Fanon considers her lack of visible parents indicative of a lack of any parents, and her lack of flight to be a disability - that bit eventually semi-confirmed in "Flight to the Finish." Here? Instead of Scoots being abused or a homeless orphan, she has a decent home, where her parents are quite alive and quite sweet. They live on the edge of town and that's why you don't see them turning up at school or before/after Cutie Mark Crusader adventures. Even the usual flight angst is averted: Her mom is a pegasus and her dad is an earth pony, and Scootaloo sees herself not as a disabled pegasus, but as an earth pony with the added bonus of little wings which she can use to propel her scooter faster and even hover a little. That doctor's office scene you've seen a million times in fanfic and fanart where Scootaloo is wailing in anguish as she is given the news that she'll never fly? Impossible here.
Fanon: Ever since the Fluttershy chapter, some have adopted Fluttershy being the author of Daring Do as their headcanon.
Hilarious in Hindsight: The Newhart-style ending with an infant Twilight hugging a Scootaloo doll is even better upon reading the sequel, Crisis Of Infinite Twilights, where Baby Twilight joins the cast.