As some one who has some Balls with and without the compensated nut I can tell you that the improvement in intonation all the way up the board (at least to my ears) is subtle. Most people who are listening in the audience won't be able to tell the difference in intonation. So all I am saying is that the compensated nut is nice to have, just not a huge necessity for me.
All my life I've been told by music instructors and others that I have great ears. However, I can't tell the difference with and without the compensated nut. Either my ears aren't so great, or the difference is very subtle. I wouldn't hesitate buying a pre-comp nut guitar for a second...
As far as differences between the old and new JP6 (not counting the BFR), I have an old one (2005), and a new one on order. I love the old bridge pickup, and the harmonics are especially good. So that wouldn't be a decision point for me either at this point.