Well, it depends specifically on the sound you want.
The Super Distortion is very blunt and raw, but still retains its PAFishness.
The PAF Pro is a much more rounded, expressive, organic pickup imho.
Don't worry about output, this is a common misconception. You can play metal on a vintage output pickup if you want to; all output means for practical use is how easy it is for a pickup to throw a tube amp into overdrive, or sometimes distortion. Higher output pickups distort easier, this doesn't mean you'll get more or higher levels of distortion out of a high output pickup. If you have an X2N (510 mV of output) and are not playing with any gain, it really won't distort. Distortion comes from a pedal or preamp.
So it's up to you. Decide based on tone. The DiMarzio sound clips pretty accurately depict the pickups, especially "Frantic" by Dave Sharman for the Super Distortion (although that's also hte bridge, so in the neck the super distortion ill be a bit more rounded) and "En Aranjuez con tu Amor" by Fredrico Miranda will give you a very good picture of what the PAF Pro sounds like.
And both will give you a wonderful
shred tone.