Comes down to how crazy you plan to get. If you plan on doing a suspension upgrade, bigger axles and wheels/tires and possibly a motor swap than save the money and take the better deal on a 07-11 Rubicon.
If you plan a more mild build like sticking with the motor and running the 44 axles, then pay the extra money up front for the better motor and improved creature comforts of the 12-13 model
If you plan a more mild build like sticking with the motor and running the 44 axles, then pay the extra money up front for the better motor and improved creature comforts of the 12-13 model