The stock filter will protect the engine the best - bar none. It wil reliably support airflow well over stock also.
The aftermarket air filter game is about spending money for some wide open performance gains, at the expense of protecting your engine for the other 99.9% of the time. I doubt a stop watch would record any difference between stock and any of the aftermarket ones, except maybe Banks because they seem to be the only ones doing any real research. You might check out their website where they compare the different air intakes.
That stock filter is a pretty impressive piece of equipment that lasts a long time and filters very well, compared to any of the alternatives.
Unless you are competitive pulling at the high end (500+ HP) and are willing to put up with increased wear on the engine due to inferior filtering, and way more frequent cleaning intervals, stick with the stock system.