A really odd theoretical match up, imho!
First off, many believe Jones could take Anderson Silva down and submit him or mess him up with elbows due to how good Jones' takedowns are.
Conversely, Anderson Silva probably could make Bones look like an amateur in the standup for all we know.
It seems like each fighter could be the other's kryptonite, which is hard to think about either losing with both having that unbeatable aura. The beauty of such a matchup is that one is surely to lose....and probably in violent fashion. 
Seems pretty even 
I really belive they are the only two guys, HW div excluded, who can beat each other.
I say exclude HW cause I think JDS would throttle them both!
AS is scared of JBJ. He makes this very clear
"Conversely, Anderson Silva probably could make Bones look like an amateur in the standup for all we know."
Jon Jones has crushed strikers in the past. Easily too.
And he has a 7 inch reach advantage against Anderson.
It doesn't matter if you have 15 years of experience with MMA muay thai. Nor how long a list of names you've defeated in the past. Jon Jones nullifies that, and everything else, and just destroys.
I give Anderson almost no chance against Jon Jones, Anderson shouldn't take that fight, it would be terrible for his legacy, and why should he? He shouldn't have to fight out of his weight class to prove anything, he's a MW, and he's the MW king. He should go out like that.
I would slightly favor Anderson in this fight, although its definitely his toughest fight outside of hW.