The JK has better on-road drive-ability, comfort and safety features than the previous generations of Wranglers. Plus, you can get it in a 4-door, which for some of us, was a HUGE deal.
In the US, JK's only came with 2 motors the early 3.8 and the current 2012 and newer 3.6. Of the two the 3.6 is preferable. If you have the cash, you can swap the 3.8 or 3.6 out for a Hemi of Chevy LS V-8. Supercharging either the 3.8 or the 3.6 is an option as well. Definitely, if you get an older Jeep look for the 4.0 straight 6. IT is one of the best motors of all time. 100k on a well maintained straight 6 is not a big deal, to me at least.
Auto or manual is really personal preference. I like my manual, but many guys wheel hard on the automatic slushboxes.
As you upgrade, you will lose mileage. Bigger tires and heavy bumpers/equipment increase weight or drag. There's no good way around it. Supercharging, and gear changes can help, but nobody's getting "great" mileage in their JK, unless maybe the have the European diesel.
It's possible to modify a JK past the point where reasonable people consider it a daily driver. I don't know exactly which one(s) in the sale section you are looking at, but after some point, the more heavily it's modified, the more likely there will be some daily driving drawbacks.
'76 CJ-7, '43 CJ-2a, '78 Bronco,'78 CJ-7, '75 CJ-5, '78 CJ-7, '80 CJ-7, '78 SJ, '79 SJ, '78 and a '76 FJ-40 , '90 XJ, '91 XJ, '86 CJ-7, '95 ZJ, '68 CJ-101 Commando, '00 TJ, '68 M-715, 2 '86 Military Blazers, '96 LR Discovery, '86 CJ-7, '91 YJ, '99 TJ, 07' JKU Rubi, 1988 YJ, 1973 Commando, 3 Diesel Excursions....
Now back to a 2013 JKU Rubicon with "stuff", planning 37's with minimal lift.
I've tried them all... Jeeps are still the best. (0||||0)