I've only driven a 2.0 Rubicon and a 5.7 Rebel with the BSG, so this isn't a spot on review of how it works on the 3.6.
I will say that the start/stop operates much more smoothly with the BSG than any 12V start/stop vehicle I've driven. You also notice very little turbo lag in the 2.0 but that won't matter with the V6.
I’ve only driven mine for about 160 miles, but love it so far. As mentioned above, the start/stop is nearly imperceptible. I have driven other vehicles where I’m looking for the button to turn it off, not in this one. The initial pickup off the line is really good, throttle is almost too responsive... no problem spinning the BFG 33’s (I have rubi take offs on it) if you are not thinking about it at launch. Passing is really good as well, although still in the break in period, I’m taking it relatively easy.
There is more plumbing under the hood, three coolant overflow tanks instead of one, besides that and the missing alternator, looks like another JL 3.6 engine bay.
I love it. I currently own another 2.0 direct inject turbo, and didn’t want another - very happy with our choice!