This guy did it on his tj so it should be pretty straightforward on a jl. Good luck.I don't think there's evidence to say that a 3.6 or a 3.8 with a supercharger is going to be more reliable than a Hemi. I think they're both pretty reliable from what I have seen.
You're right about emissions -- it will be difficult to pass in certain states such as Nevada and California where referees are involved, etc. My Hemi TJ went through the emissions process in Nevada, and it was time consuming. However, the swap was done right and it passed without problem. California is trickier (and an LS swap will never pass). Have had no issues in Arizona but that should not come as a surprise.
That said, saying that both are trash swaps is a bit of a dramatic statement (not even sure what that means, so I'm guessing). If done by a reputable shop at this point, you really should not run into any major issues, assuming you are sticking to the formula that's been repeated over and over -- including any tuning requirements. Also, the harnesses have also had their foot print shrunk to the point where it's pretty much plug and play. Stray from that repeated formula and ALL bets are off. Also, cooling capacity is extremely important, and things like fender liners, grill modifications, winches blocking air inlet, and weight will creep up FAST.
But yes, it requires more headaches, more money, and more time! However, for those wanting something unique -- it's worth it for many. But you need to know what you're getting into. For ~99% of people, the supercharger option is fine.