I have been really happy with the stock pickups, especially the neck although I know I am probably in the minority.
I think PRS pickups are very good, the people there know what they're doing. We tend to get carried away on here, saying everything needs replacing with BKPs, but there are loads of other great pickups in the world.
Having said that, I am replacing the pickups on my Mira - with Cold Sweats as it happens - because the stock ones are just a little too warm and vintagey. I want it to be more of a rocker.
The RPs are really, REALLY nice. Put them in a stoptail Cu22 and you'll not be disappointed! Great definition and immensely, um, immense sounding. Matched my old Mesa Recto great - the combination of slightly vintage pickup and modern amp worked. OK I've since sold both the amp and guitar but that was a usage vs cashflow issue, nothing to do with the tone! :(
HFS/VB... The VB was a little sterile, and the HFS seemed a bit uncontrolled. The CS set fixed both of these points - livening up the neck position and giving more definition at the bridge. My opinion, anyway, and the rosewood neck may have introduced some characteristics that didn't agree with the stock set. ;)