For what it's worth, here's my 2 cents.
I owned a few different Wolfgangs, and then switched to the Axis, which I perosnally thought was a better guitar. I played the Axis for over a year, but always thought that I was missing out on something because I didn't own a PRS.
I had an opportunity to trade my Axis +$200 for a 1994 (pre-mass produced) PRS Custom 24, so I jumped at the chance because I had always heard how great PRS was.
I thought the set-up and playability of the guitar was good, but I noticed right away that there were certian spots on the neck that didn't sustain as well as my old Axis. I also thought that the acoustic tone of the guitar unplugged wasn't as resonant as the Axis. I didn't let it bother me too much because I thought I owned the Rolls Royce of guitars.
The PRS does have excellent playability and intonation qualities, and it is a beautiful guitar. For someone that plays mostly leads, I believe it is probably one of the best guitars one could get.
Now is where the story takes a turn. I was really happy with the guitar until I played my first gig. I play mostly rythym, and spend a lot of time holding chords at the far end of the neck. I started to notice at the beginning of the third set that my hand was really fatigued. I wrote it off as just getting used to the neck. After the same thing happened at every gig for a month, I started to think there was a little more to it than just getting used to the neck.
I started to examine my hand position on the PRS vs. my hand position on the Axis. I found that my wrist was kind of cocked at an odd angle when playing chords at the end of the neck on the PRS. I believe it is the overall length of the guitar that puts the end of the neck a little farther away that caused my problem.
The problem didn't go away in 2 months, so I went to Guitar Center and traded it in on a Purple Axis, which I swear by and play to this day.
I've owned both, and I personally prefer the Axis. I've played a lot of Ernie Ball stuff at guitar stores, and I've never found a guitar that sounds bad, or is set up wrong. Every Axis I've ever played pretty much plays the same as any other one I've tried.
I've also tried a lot of different PRS guitars, and think that they are also pretty consistent, and high quality guitars.
The conclusion is that they are both high quality guitars, and it's really up to your personal preference to decide which is better.
IMHO, the quality of both instruments is top notch, and the biggest difference is price. I feel if you can get the same quality for $1000.00 less, that would be the way to go. My individual preference is the Axis.