Wasn't one of the big theories that the Waif was actually one of Walder Frey's bastards? Personally I like that theory more as it explains the outright animosity the Waif has for Arya. If it so happens that the Waif is a Frey (or a Rivers), why would she bother to complete a Stark hitlist? In fact, even if the Waif isn't a Frey, what would be her motivation to complete that hit list anyway?
The other reason I don't like the theory is the latter parts of the series seem to be playing out like an outright Stark redemption story for all the **** they went through basically from the time Joeffry took Ned's head through when the Night's Watch betrayed Jon Snow. Look at them now - Jon Snow is actually insert Valyrianesque name here "Jon" Targaryen, son of Rhaegar Targaryen and Lyanna Stark, named King of the North with an at least somewhat legitimate claim to the Iron Throne (although he doesn't know most of this yet - but Bran does). Sansa Stark has grown up to become the Stark's politician that knows how to play the game of thrones. Bran for all intents and purposes is the new Three-Eyed Raven (whether that actually happens or not, we'll see). For Arya to actually be an Arya-faced Waif would be a kick to the stones of the Stark revenge tour.