Outside of the fact that she was bullied for her appearance, there's really nothing to suggest that Arya is ugly. Catelyn does say that she isn't as pretty as Sansa but the emphasis was on how messy she was from playing and her state of dress. Her remarks on Dacey Mormont ( who has a long face like Arya's at that) being pretty when she put on a dress instead of armor make it clear that she associates traditional feminity with beauty. She even tells Arya that she could be pretty if she weren't so messy and dressed properly.
The fact that this is such a debate in fandom when it's written plainly in the books is crazy to me, but I guess people just need this little girl with self-esteem issues to be ugly or they can't cope.



fromtheseventhhell