Is because he no longer trains with Greg Jackson and Winklejohn as his coaches.
Everyone hypes up his talent and natural gifts but a big reason for his title win and title run is because he had the best coaches in the business at that time. You really saw it when he was fighting Machida.
Towards the end, Jones was declining as competition at LHW got more stiff. He no longer had dominant wins against top-notch competition anymore and a lot will say he even lost against Reyes and Santos.
However, it was Jackson-Wink that carried him to the finish line.
I think without them, Jones is a mediocre fighter and an overrated champion. They were probably the biggest reason he had the run he had.