Most of the ponies are flawed somewhat, especially Rainbow and Applejack, so I find wars between their fans funny. Applejack is too proud and her stubbornness alienates alienates her from her friends. Twilight is condescending and overly skeptical of things she can't explain. Rainbow is a selfish bitch. Rarity is shallow.
I can't think of any negative points for Pinkie or Fluttershy. Out of all of them, Pinkie consistently has the best attitude and even questions herself if she doubts her own attitude, which can be said for none of the others (except Fluttershy and Rarity who haven't really been put in such a position yet).
That said, Twilight is still my favourite pony. She's just such a badass.