Seems to me that everything I've read says that aftermarket is better. Better exhaust flow = better performance, gas mileage, etc.
Month or 2 back, JP had an article comparing aftermarket cat-back exhaust systems. They range from quieter-than-stock, to hot rod rumble, and all are supposed to be an improvement over stock in performance.
Where is the leak ?
The cat-back systems are mostly bolt-on, and not too difficult.