Hey,
Its pretty much a toss i think, SM being more warm and bluesy and Mules being more middy and suitable for vintage types of rock. Still the Mules are likely to do it all.
The standard mule set i have is unpotted and have even less feedback than my stock gibson pickups so dont let that keep you off them, the unpotted ones have a very pleasant high-mid focus, very smooth, very tight bottom. Actually the real PAFs i have are a bit grittier and more 'raw' so to say allthough the neck Mule is pretty close and probably will get spot on after a couple of years playing.
I have the mules set up for neck lead and bridge rythm, i think they are especially suited for that as they are very sensitive pickups, if you want a more agressive bridge lead tone i wont go for a mules set but rather a neck mule and say a Riffraff or even VHII bridge.
Dont think the bridge mule is a wuss now though, if you know the fine art of boosting a pickups signal youll have such a good time with the Mule bridge, you can just pile up any gain level you want and it wil take it, full out metal? NO PROB!
Still, for that warm bluesy PAF tone i would recomend the SM, and by the way GnR have some of Tim's SM's too, so.......
PS. I have unpotted and covered pickups which Tim has a special trick for to make them way less prone to microphonics, i dont know how unpotted and uncovered would be......