I am going to have to agree with wouldluv2fightu on this about the level of competition. BJ certainly gets the edge with Machida (Ko'd Rich Franklin) and GSP alone. Because GSP lost last time he faced Hughes and everyone knows he is a better fighter now. What was his last fight? That would be the one against BJ.
As for the weighing on the fighter's mind part that someone mentioned. A champion will use that as inspiration to whip his ass next time. BJ would be at the disadvantage here because he might (doubtful) go into the fight thinking there is no way to lose and take his competitor lightly because he has already beaten him.
The only advantage I can give Hughes is work ethic. He trains harder even when he doesn't know if he is going to fight. The guy is a workhorse and BJ has been labeled lazy as far as training practices are concerned.
In the ring skill, BJ has the edge standing and on the ground. The guy has amazing balance, center of gravity, flexibility and knowledge. But, if the fight last more than one round look out for Hughes to take over.
I personally, think Hughes will win for that reason.