If you can afford it, the 3.6 (pentastar) is light years ahead of the 3.8.
I personally think the auto > manual for the pentastar. Better on and off the road. If you're not fanatical about having a manual (or just prefer manuals), the auto beats the manual in every way.
Don't get the 3.8 auto combination. its a sh*t combination. If you're going to go a 3.8 stay manual, the 42rle is not a great auto box.
I've had a 2012 auto JK, 2014 JKU auto and 2013 JK rubi auto.
I've always had my 2003 auto TJ. The auto in my tj 42RLE is the same that is mated to the 3.8. In the TJ it is just good enough, its not awesome. But the TJ is light and it does a okay job with the 4.0 (with some mods). I only mention this as with a bigger body (JKU) it would suck. it hunts around and its just not fun.
As for the diesel, I don't know much about it. I've _heard_ (take with grain of salt) the parts are expensive, and the USA doesn't get it so aftermarket parts are not as easy to get as the 3.8 and 3.6. I belive the manual in the diesel is de-tuned a touch as it cannot handle the power as well as the auto (which I believe is a better auto then the one in the 3.
. All and all, i've heard the diesel is a solid engine. But others who actually own one will be able to school you better here.