Certainly everyone knows Shogun would've been better if he didn't have three knee surgeries. He was still good enough to be the current champ when Jones beat him.
Machida couldn't hang with a new generation of big LHWs?
He left the division losing a questionable decision to a large LHW. He also starched Ryan Bader who was just as big and beat Davis twice afterward. Lyoto was a small LHW, but that's a weird way to describe him in an attempt to discredit Jones' resume.
He's one of the greatest in the same way "prime Mike Tyson" is one of the greatest boxers. His ability is undeniable and there is a strong argument to be made that he was the best to ever do it at his peak. His career/resume simply doesn't stack up, though. Not even close.