I just purchased my 3.73 auto and am feeling the EXACT same thing. Did the problem ever resolve for you on its own after 1000-2000 miles? I am certain I did not feel this in the 3.21 during a test drive.
(Your post in May 2012)
"Howdy. Now that I have had my JKU for about 4 days, I'm ready to ask another question to all you fellow Jeepers.
I notice that off the line my Jeep is pretty smooth. However, when I get to what feels like the second shift point, the Jeep really feels like it hits a bit of a wall in the throttle response. If I baby it and try to smoothly accelerate, it does shift, but not very smooth. If I don't think about it and just keep steady on the gas (no stomping) it also feels pretty rough at that shift point.
Does anyone else experience this? Could it just be the way this auto transmission is or the combination of 3.73 that creates less than ideal shifting characteristics?