I think Silva has better skill set as compared to Jones (multiple black belts in: Muay Thai, JiuJitsu, Judo, Tae Kwon Do AND a professional boxer). I also believe Silva has the added experience that Jones might lack in order to get out of bad situations.
Jones, on the other hand, is younger, taller, faster, stronger and might very well have better stamina than Silva. Jones is also incredibly talented in his overall ability to adapt to his opponent's strength, while exploiting their weaknesses.
Keep in mind, that Silva is Jones' hero. While he was growing up and was simply a fan of the sport, he modeled a lot of what he did after Silva's approach to MMA. He is probably one of the fighters that can predict a lot of what Silva's game will be come fight time.
By way of sheer odds alone, Jones would defeat Silva. My take is that Silva's experience, couple by the fact that his height and reach are slightly comparable to Jones (Silva is 6'2 with a 77.6 inch reach, Jones is 6'4 with a 84.5 inch reach), could very well provide an upset at the end.
I would love for this fight to happen!
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