For a lot of critics, it really is all about the drugs and the fact that many of Jone's most notable wins were against so called Old Gaurd LHW fighters who were by and large shot by the time Jones faced them. And the multiple drug busts put into suspicion some of his wins before USADA laid down the law and started their strict enforcement. Given the physique he's had throughout his career, we can't discount the possibility he was using various illicit drugs through his whole LHW title reign, including the first fight with Cormier.
It's also why Anderson is often considered still in the all time best tier, naturally, but is much less often included in discussions of the one true greatest ever. It's now largely become a battle between GSP and Fedor.