I just drove my first TJ yesterday and I have to add one difference that really bothered me vs. my YJ. The seats on my YJ sit up about a foot from the floor board while the TJ seats are right on the floor like a car. I noticed that I didn't have the same view over the hood and dash like my YJ.
This might be all in my head but the 4.0 automatic I drove seemed anemic in the torque department compared to my YJ too.