My Hemi Jeep has 4.88's. 4.88's are fine but 5.13's might be be better.
The lowest you can go in the current Rubicon D44 is 5.38's, 5.13's in non-Rubicon D44's. That is not enough to make up for the 175hp, 135lbs' defecit, and not nearly enough considering the even larger torque differential at lower RPM's. Remember, any Hemi has more torque at 1200rpm's than the 3.8 puts out at max.
Re-gearing only makes up for so much hp/torque defecit, it can't cure the 3.8's woes, especially since the 3.8 is an engine that likes the rev's rather than one that puts out at lower rpm's.
As far as loosing top gear, only if the Jeep is woefully underpowered to begin with. If the engine has enough torque and the re-gear is approriate for the tires/engine combo than there is no loosing top gear. For example, my Jeep turns 2150rpm's at 70mph in top gear. It will maintain that speed with minimal downshifting through rolling country. The 3.8 set up similarly will be downshifting at every highway overpass, slight grade or even when bucking a head wind. (On top of that, the leap from the 1:1 third gear to the top .67:1 O/D makes every downshift an overwrought and dramatic event, whereas the five speed 5-45rfe which the Hemi mates to has a third speed 1:1 and and O/D fourth and fifth, eliminating the drama on downshift.)
Here is an example of what adequate and more torque can do: I visited River Raiders' Off Road in PA to have them install their aluminum skid package and to fab an aluminum skid for my Long Ranger Auxilliary gas tank - extends range to almost 500 miles, great tank! I had an evening to kill and visited Getttysburg Battlrfield, had dinner in town and headed to my motel about 30 miles west, over a relatively low range of mountains where the Appalacian Trail runs along the top ridges. The road was empty and speed limit was 45mph. I set the cruise control at 50mph, which gives a mere 1500rpms. Through the rolling countryside, over the low mountain and across more rolling countryside. The Jeep maintained 50mph, never downshifted, never lugged or bogged... The drama with a 3.8l would have made the drive a pita rather than a peaceful, quiet opportunity to ponder the great courage and the great loss, Lincoln's fantastic address that the battle and its magnitude in scale and importance to our history requires.
Rumbling along without issue or drama at 1500rpm's and at 50mph might seem to have on-the-road-only relevance, but its illustrative of the huge benefit of torque off road as well. For example if the engine has enough torque at 1500rpm's to push the "flying brick" along at 50mph over hill and dale without complaint or downshift or drama imagine what would be possible at 4mph, which is 1500rpm's in 4low and first gear.
BTW, my wife has a pretty stock '08 four door Rubicon still running its oem tires. It has 4.10 gears. I can be reminded of the 3.8l's shortcomings compared to the 5.7's benefits whenever I want.
JPK