I prefer Twilight as the Doctor's companion more than Derpy. It just makes sense to me but, I do see the appeal of Derpy. I like to think that what happens is the Doctor crashes in Equestria, meets Twilight, travels with Twilight, meets the other mane 6, travels with mane 6, then has an adventure where he has to save the mane 6 with the help of Derpy. Derpy becomes his companion, then the Doctor is Discorded on his last adventure with Derpy. Derpy leaves him, and Twilight grows closer to him while trying to find a way to turn him back to normal. It goes in a complete circle.