I just did what you are thinking about. Sold my pile of crap 2004 Dodge 2500 Cummins and moved into a 2012 JK Unlimited. I DO miss the towing capacity of the truck enough that I snagged a '96 Ford PowerStroke for truck duties. I used to daily drive the Dodge and while it's more civilized to drive everyday than the '99 Ford F250 it replaced it was still a truck in the city. If I lived a little more rural, I think I would have not noticed the truck as much.
I DO like the 2012 JKU with auto and would definitely steer you towards a 3.6L Wrangler or a Hemi or LS swap for the 3.8L (my experience would be 4 door---the 3.8L may be OK with a 2 door?). It's just nicer to deal with everyday. I don't have to find a diesel pump at the filling station. I don't have spendy oil changes on servicing. I can park pretty much wherever I want to and can move in/out of traffic fairly easy. I LOVE having a warranty after fixing the 2004 Dodge all the time. Even with the stock 3.21 gears and 35" tires, the JKU is manageable in traffic. I need to spend some time in the garage and swap my axles to the 4.88s with ARBs but just haven't had time to do so this summer. I imagine the Jeep will scoot quite well with the 4.88.
I MISS the torque of the Cummins. I don't miss the truck it was wrapped in at all. The '96 that I bought for actual truck duties, I really like. I bought it cheap enough I don't mind repairing it as I think I'll get my $ out of it via use. If it goes to worms, I don't have much $ invested in the truck anyway. I DO miss the comfort while using the truck of the 2004 Dodge vs. the '96 Ford. The Ford makes no apologies about being a truck. It is a 1 ton and couldn't care less what you think of it. Loaded down, it rides pretty decent. Unladen, the thing is a roller skate (how it should be).
In short:
My solution was to sell the 2004 Dodge, buy a 2012 JKU and buy a cheaper old truck for truck duties. I did that in Feb. 2012 and have liked the compromise so far. YMMV as your Dodge is a much different animal than my tow pig Dodge (leveled with 285x17 BFG) and it depends on what you're wanting in the JK.
4 doors started in 2007 with the JK redesign. The 3.8L is a slug. I wanted a V8 version so I drove a few intending to swap an LS1 or Hemi into it. I drove one 3.6L and decided I'm OK with the warranty and the smaller, peppy motor.