3 category break downs aren't nuanced enough.
Yeah, maybe Rua has more experience on the ground, but he is always going to be on the bottom, against a guy who is much larger than him and can throw fight ending elbows. Jones ain't no slouch in terms of his BJJ either. He has shown great top control. Even if Rua manages to standup, he will probably still have Jones attached to him and get taken down repeatedly.
I dunno, I haven't seen very much of Rua's bottom game, just a couple heel hooks and the like, but heel hooks are SOOO 2001. I'm not convinced that being on the ground will be to his advantage or even neutral.
The stand up is where Jones is going to be challenged the most. The only comparable person to Rua who Jones has faced with quality Muay Thai is Vera, and Vera doesn't count because he's Vera.
I find it hard to breakdown Jones striking because it's so unique. The main thing that is a constant however is is range.
If Rua wants to cause damage he's going to have to move inside, and I'm pretty sure if he does that, he's going to get taken down.
Legs kicks might work, but Jones will be looking to catch them. It's a risk when one take down can lose a whole round or end the fight.
So yeah, from the outset I say Jones has the stylistic edge due to fact that he can dictate where the fight goes.
Shogun's best chance is to mix his strikes up, leg kick when certain, move, stay away from the TD, and go for a power counter if the oppurtunity is there.