I think it was a combination of ring rust/gas, getting hurt early, and JJ's massive strength. Shogun definitely did not look the same after the first JJ takedown though. That being said, even if it was ring rust, recently repaired knees, or simply getting hurt early and never really recovering, I'm not sure if Shogun is able to beat JJ even if he was 100%.
I can't wait for someone to smash JJ and bring him some humility the hard way. I was never a fan of JJ's personality but at the same time I never disliked him either. His talent made up for the douchiness factor. But after the disrespect to Shogun who's one of the classiest guys in MMA, I can honestly say I will always root against him. Regardless how I feel about his personality, I still admire his talent, and know that he had very few people that will challenge him at 205.