I have had the complete opposite experience (and almost everyone that goes from a 4.0 to a 3.8 will agree).
Likely, most of the experience that the 4.0 is peppier is from the actual throttle cable.
But, with that said, I am running the EXACT same tires on my Cherokee as my parents had on their JK.
3.55 Gears, Auto Transmission and 120K miles - my Cherokee has no problem maintaining 55 or even accelerating.
My parents JK Rubicon with the SAME EXACT tires, couldn't maintain 55 on flat ground in 6th gear. The only time it could use 6th gear was going down hill.
The only way to accelerate from a stoplight and keep up wtih traffic was to wind it up to 4K rpm. The old 4.0 could do it, easily, below 2500.
The 3.8 is a rubbish, underpowered engine, in my experience.
Lot more fun to drive, though. Never had to wind up the 4.0 and shift all the time. Their 04 Rubicon didn't even need 1st gear - it could take off in 2nd all day unless you were on a steep hill.
I would like to test drive another 3.8 6 speed to see if they are all that bad.
My Cherokee with 31s and 3.55 gears has no problem accelerating and keeping up with traffic without needing to red line. Unfortunately, I can't go above 3000RPM because the fan clutch causes the belt to slip.
I'm not saying the 4.0 was perfect. It didn't have a lot of power up top, did have a habit of dropping piston skirts and cracking heads (all year susceptible to it), drank gas and liked to mark its territory.
IF the 3.8 didn't have the bearing problems, you could run a cable to the throttle body *and* you could get rid of the sub-par chrysler electronics, I'd be first in line for an 07JK for a toy. I still may consider one.
Aside from engine and electronics issues, the JK is much better in every other aspect than what it replaced.
It rides MUCH MUCH better on the road, but, is MUCH more capable off road. The "long arm" suspension (longer arms than a TJ) just does everything better. And they can fit much larger tires from the factory. And I can comfortable fit in one.