Those systems are very comparable in price used, really can't go wrong either way.
With the JB3, you can update it to 1.3 or the latest 1.4 beta for free by sending the chip in to BMS to be flashed, or having someone with a burner flash it for you. So you'll have a fully supported production system. 1.2 is pretty invisible but 1.3 is much better, so update it if you go the JB3 route.
NEW PERFORMANCE LINE N54 DOWNPIPES & M3/M4 & F30 ER DOWNPIPES NOW IN STOCK - ER N54 CHARPE PIPE SPECIALS - NEW JB4 G5 ISO for N54 and F30 N55 ON SALE - NEW S55 M3/M4 JB4 NOW SHIPPING