For me, one thing that I've noticed that differentiates Harden from a lot of other players is that Houston predicates it's offense on getting Harden the ball.
Note that I said getting him the ball. Which is completely different than running an offense through Harden after he's gotten the ball.
One of the most fantastic abilities that Kawhi has is his ball denial. He's a monster at getting to his man, cutting any kind of passing lane out, and limiting effectiveness. It frustrates a lot of offenses that don't start until their star has the ball in his hands. If they never receive the ball unless they are pushed up against the baseline, or in a crowd of defenders, it severely reduces their effectiveness and the offense starts to congest. We saw this against Golden State -- the instant they got out of position they were looking for outlets to swing the ball around, and Kawhi got several steals from that situation alone.
For Houston, they work TO get Harden the ball. Which means it's a LOT harder for Kawhi to cover him. Anyone who's played basketball knows that if you have to fight to get out on your man, the moment you land and set your D, there's the briefest of instants where you are catching your balance. Harden is fast enough with his first step to take advantage of this. And as good as Kawhi is, he's still a human being and has to account for his own momentum.
Watch the Rockets play and you'll see Harden is already going into his shooting/driving motion by the time the ball is thrown in his direction. This differs a lot from, say, the Thunder, who pass the ball out to the top of the key, the defense sags a little to respect the open lanes, and in doing so gives someone like Westbrook or Durant all the time they need to get picks and read the defense.
Harden is brilliant in keeping defenders off balance by quickly using attack windows that only exist for a brief second. In practice, it looks almost identical to say, Westbrook just blowing by someone, but the physics are quite a bit different, and it's really at this point the only way you're going to beat Kawhi to the rim, he's too long and too quick to just ISO and go against. Someone transcendental like Jordan could have rocked him off his defensive stance, but none of these guys are even near that level of footwork and prowess. As it is, Houston is tough because they use the passes to their stars as weapons themselves, instead of allowing the D to set and overpowering them.