I cant answer any of the other questions for you, since I have an older TJ but I can answer the one about gas mileage with the older Rubicons.
It seems to vary (obviously based on driver). I seem to be getting 17.5 with the top up, 13.5 with the top down, and 14.5 with the top down and the back seat out of the vehicle, or even tumbled forward.
Latley I have been riding with no doors and no windows but the top up, kind of like a bikini top, and I seem to be getting closer to the 17 than the 13.
Some people claim to get 18 with the top up, but thats usually about as high as you can get a Rubicon p**** footing it. Some say they get 14-16 regardless if the top is up or down. YRMV
Its not great, but its not an 8.1L crew cab long bed pick up either. If gas is an issue, get Jeep out of your head right now. Its my ONLY complaint with the rubicon (which by the way is going to get worse gas mileage than a sport because of the gearing). A 6 spd(05-06) also gets slightly worse gas mileage than the 5spd(97-04) because of that .86 sixth gear. Although the 5.06:1 1st gear is real nice
(nice in rocks/hills off road).
As far as Manual Vs. Automatic.. well I dont know much about the new one but as far as old TJs go this is how I think of it.
For rock climbing, or strictly a mall cruiser that wont really see off road (basically NO mud/water) Automatic and manual is kind of personal preference.
For mud and water crossings (like on most the east coast..) manuals are better because automatics HATE water. If you get some water in an automatic transmission, its likley to not get you off the trail and be a costly repair. A manual will atleast get ya home
Your cons with manuals are obvious, traffic stinks, injuries stink, but you gain lots of control off road
Its all personal preference I think. But anywho, someone will chime in with the new JK stuff soon, I dont want to give you false info. BTW, Welcome to WF!!