Having owned 3 different 4 cyl YJ's, and a 6 cyl TJ, and currently my '11 JKU (and many other Jeeps along the way), I can say from experience i'm very happy with the 3.8 engine.
Reading up before buying, most all the complaints made it sound like it was the worst dog of a motor ever produced, unable to get out of its own way. Many still say that.
Personally, I don't get it. Mine has the auto behind it, and is in the heavier 4 door, and I still think it's just fine. It's smoother than the 4.0 ever though of being, and the mileage is great. I drive tamely, but up/down hills all the time. The tranny downshifts/upshifts fine, IMHO, and I absolutely love driving it.
To be fair, I wasn't expecting V8 power, diesel torque, or turbo redlines, so perhaps my 'normal' expectations met my results?
I would NOT be happy with 3.21 gears (I have the 3.73) but other than that, I like it just fine.
Many preferences are subjective; I'm not taking anything away from those who love the pentastar, new trans, or higher regear- this is just my take on the issue.
Good luck in your search- whatever you choose!