Just got my new 2012 Rubicon last week. I got it loaded to the gills, and will be making a few modifications over the next couple of weeks to finish it.
First thing I did was change wheels and tires to Black Diamond Viper 900s (17" with 4.5" backspacing) and Toyo Open Country 295/70. The vehicle is not lifted, and I don't plan on it. Tires/wheels work great - only slight rubbing when wheel is fully turned right / left.
I am very pleased with with new engine. Already took this on a road trip (to escape Hurricane Irene). The new engine packs plenty of power (even with automatic transmission). I was able to accelerate just fine up hill, into the wind - cruise control managed just fine, passing vehicles on highway just fine. Gearing favors highway - i was pushing only 2,500rpm at 70mph... 18-19mpg average.