I personally don't like it when NPCs are dramatically rules different than PCs. I also don't think the Big Bad has to be a fight in and of itself. That's very D&D thinking IMHO, where you put 1 foe against the party and everyone whittles down a big bag of hit points.
Consider the ending to the old Flash Gordon movie http://www.youtube.com/watch?v=sa_p9Up9DFg
Pretty much a 1 hit kill on the big bad. But it's the scene that's epic, not the kill. Lasers flashing, people running everywhere, another PC attacking a room to get the lightning shield and defenses down, the ship crashing, etc.
If I did an evil clown villain I'd build the scene, not the foe. They see posters of the clown as they go through the carnival. Come onto scenes of death, and run into minions twisted and warped by his insanity. Every now and then an evil laugh would follow the PCs, but they could never quite track it down. And in the "final" encounter just have lots of minions, maybe some situational timed thing going on(dramatic task to solve) or some sort of new evil trained monsters he finally lets loose on the PCs.
The big bads aren't big because they're tough in SW, but because they surround themselves with a twisted mess the PCs have to push through to finally take them down. And even when they do take them down their legacy can linger on.
Even if they cap the evil clown in 1 shot in the 1st round, so what? His minions are still rushing forward and the missile full of his Make People Insane chemical is still counting down to launch at the city.