Wow I guess I really haven't debated these two before.
For me, Pros and Cons of FJ:
PRO: Queue, ride system, I find the story fun, unpredictable ride (anytime I ride this attraction I always forget something or two, because SO much is going on!), and again, Queue. It gets bonus points for being so good.
CONS: Ride itself can make me feel a little ill afterwards, never been sick but not as fun to ride over and over again, screen use is well done but not great.
Gringotts
PROS: Queue, Ride itself, story, thrill factor, theming, ride vehicle
CONS: Just a tad short, wish it was a little longer. Not as unpredictable and not as many things going on at once.
I guess overall for me its Gringotts. I just love love love that ride. FJ is the closest #2 possible. I have the right to change my decision, though. Gringotts felt like a more natural ride I guess. Really curious as to where Hagrid will end up here though. All are A+ attractions.