FWIW.........
If it was my money, and it's not....I would buy an Unlimited with an auto. I base this opinion on the fact that I have had two SWB Rubicons, both manuals - one each 5/6 speed. We have sand where I live and I could never seem to make the engine happy when in the sand. In low range, to get enough wheel speed, you need torque in a higher gear or engine speed in a lower gear. There just didn't seem to be a happy medium with the gear choices available - the engine was either rev'd too high or luggging. I believe that for most wheeling, with rocks being the exception, you are better served with the standard transfer case.
I have driven LWB TJs and believe they are much better suited for a DD and would also be great on trails. After two TJs, the LWB would be my choice.
My choice of the automatic is because the auto should help overcome some of the loss of gear multiplication in the stock transfer case. A slipping torque converter has the same effect as lower gears, so my theory is the auto should give back some of the low speed advantage given up in the transfer case.
I believe the automatic Unlimited would be as good a choice as a manual Rubicon from a gear ratio standpoint.
Of course the lockers really make a difference and if you don't want to build one yourself or are not able, then the Rubicon would win hands down. With a 2" BB and a 1" BL, they make a great and inexpensive forest service road Jeep!