JPFreek is one of my favorite off-road publications, and I think they did a great job with their review of the 2012 Jeep Wrangler.
I've driven 3.8-liter Rubicon Unlimiteds on both stock tires and 35-inch tires with stock gearing, with both the 4-speed auto and the 6-speed manual; it is my experience that a bone-stock Jeep with the 4-speed auto feels much more anemic than a lifted 6-speed manual Jeep with 35's and stock gears - that's how big of a difference there is in performance between the two transmissions.
My advice is that if you want a manual transmission Jeep, you might be better-off buying a used 2007-2011 model and saving thousands of dollars versus a 2012 with the new engine. This is the route I went when I saved $14,000 buying a used 2010 versus a new 2012, and to this day I'm still pleased with this decision. However, if you have the money for a 2012 model, I have no doubt that you will love the new powertrain and upgraded interior.