You can't use the end of somebody's career to discredit the beginning. BJ Penn is similar to Roy Jones is in boxing.
In 2009, he had already had a MMA fight career of 9 years. He fought the #2 LW in the world in his 2nd ever MMA fight, he fought for the title in his 4th.
He was 16-4 i believe, with his only loss at LW to Pulver (in his 4th fight ever), which he avenged. His other losses coming above his natural weight to GSP, Hughes and Machida.
He was champion in two weightclasses, with a win over the 2nd best WW. And I think 3 title defenses at LW.
His career after that year was awful, no doubt. But his legacy and standing was already cemented at that point.
(I'm not fact checking on Sherdog right now, so my above points may be a little off. But you get the point.)