Having been to both Goodwill Blue Hanger locations in Austin several times now, I think I am qualified to tell you this:
The North store is far, far superior than the East store. It has AC, indoor bathrooms (that are not bad at all), it's not as crowded, the staff is nicer, and the selection and prices are just about the same. Also, they don't run out of carts and there are always parking spaces. Can't recommend it highly enough.
But don't go there and get all the good shit before me!