I agree that PDF on 6" devices isn't a nice experience at all! It's "less bad" on the Sony though.
Rooting the Nook shouldn't be too difficult, but beware of your version firmware if doing it or you could find yourself in trouble! (I know from personal experience! Sorted it out, but there were a few scary moments there... Since I really didn't see much advantage in rooting it I decided to stay with it as it was.)