There's nothing really wrong with Jones' fundamentals. He doesn't jab as much as he did in the amateurs and early pro career, but that's not really a technical fault, it's a sometimes tactical one. Holding your left arm down isn't wrong either. There's plenty of fighters who fight this way and have done so for decades without being called unorthodox.
What makes Roy a master is his ability to control distance, feint and set traps. The last two are things that incumbent p4p king Floyd Mayweather is no master of, though a proficient enough a feinter. So, it's what Roy does when nothing (to the undisciplined eye) appears to be going on that makes him so special.
I remember reading an interview where Alton Merkerson said he saw a decline in Jones' ability to control the pace and distance. He was not worried about Jones being significantly slower. I can't find the interview right now, but I believe it may even have been previous to Tarver II. Speed is also dependent on the platform it is employed from. Speed from a fighter like Shane Mosley or even more starkly, Manny Pacquiao, is blunt, direct and obvious in it's aggression. This is highly effective in the right fight at the right time (Mosley vs De la Hoya I, Manny Pacquiao vs Marco Antonio Barrera), but can be a detriment at other times (Mosley vs Winky Wright I, Manny Pacquiao vs Juan Manuel Marquez). Jones and Mayweather use it from a different kind of base. I don't think Jones was so much relying on speed all these years, as he was relying on his great ability of ring generalship, from which he could use that speed. I even think he still has the speed for the most part. That's not what's missing.
PS Tarver also did not knock out Jones. He stopped him. People tend to forget this, the knockdown being so devastating.
Here's a link to my thoughts on the Tarver vs Jones trilogy, which I think I may have posted here before.