This is just strickly an opinion but if the SUB and the JP are running the same, you are going to probably get the most flexibility out of the JP (Oh forum gods, please don't strike me down for saying that). The dual Barts give the bass some serious tone options and the "sterility" can be overcome with a good amp or preamp.
Now... for the flip side (and to redeem myself in the eyes of those kind enough to sponsor this forum). You will never... NEVER find better customer support then EBMM. The guys out in CA truely take care of their customers. I've had issues with Fender (why did they have to buyout SWR???), I've had issues with Ibanez, Warwick was ok, but nothing fantastic (and for the money I paid, I should have gotten better support), and Kamen Music was the absolute worst. EBMM stands behind their instruments. The SUB sounds nice, is pretty versitle and plays nice (if you like the SR neck type profiles). Now I would stress that I recommend the Active SUB not the passive one.
Couple of other factors (this is all from memory from last month):
Necks - SUB 6 bolt - JP 5 bolt (I'm not positive on this) - SUB neck felt more secure
Body material - SUB poplar - JP ash (might have been swamp ash) - the ash made for some nice mids and highs but was a bit heavier - SUB is light and comfortable
Tuners - SUB HD open gear - JP Hipshot lights I think (closed gear) - the JP tuners help keep neck dive away but I like the open gear with the bigger post
Tuners - SUB 4-n-1 - JP 2-n-3 (I hated that... ick)
Finish - SUB texture matte finishes - JP I played a natural, and saw a black one (I think they said there will be 2-3 more colors by the end of the year) all gloss - I personally don't like the SUB's matte finish, but there are plenty here that love them.
Now comes the big question again, SUB or JP... answer - a used SR

(to keep the money down - can't go wrong with it), just keep watching Ebay.