Jon Jones really does have almost no weaknesses. It's pretty crazy.
Rarely gets in a bad position, but even when TRT-Vitor gets a full-on armbar from hell on him, he makes it through the pain.
Almost no one takes him down, and the one time he had someone in the guard (Rashad, because JJ pulled guard) he fully controlled the arms and wasn't touched.
Hard to hit because of his reach, and even when someone connects with a killer shot Jones shakes it off immediately (iron chin).
He's good at distance, and at clinch-distance he's lethal with the elbows. Hardly anyone has tried grappling or been successful at it -- even Cormier couldn't do too much to him and he's the best grappler in the UFC.
The only times Jones has looked bad is when he wasn't motivated (Gustaffsen I, Lionheart, Thiago Santos).
I will say this: He has no weaknesses in the octagon. Outside the octagon, he has substance abuse issues and other mental/emotional problems that have forced him to take time off, and when you don't fight, that degrades your career and reduces your rating as a fighter. So maybe that's his weakness: his extensive set of out-of-the-octagon issues.