I'd read in a Jeep brochure that the throttle response coming off-idle had been tamed - and it's true. It's more abrupt in my 4.0 TJ - kind of jerky and too fast a ratio. It's like Jeep dampened the JK's ratio and made the throttle cut in smoother.
And, the engine seems to recover from low-idle situations better. If I'm letting out the clutch and the revs get too low, I can feel the engine bringing up the RPMs smoothly without the idle hunting around.
I also think there's a difference with the cold-start program. Both my 4.0 TJ and Grand start and idle pretty rough when temps are below 20 degrees F. The JK's 3.8 starts and idles as though it's no different than any other warm start - smooth. I do notice the 3.8 takes a second or two longer cranking than my 4.0s to fire up - and I figure that's the computer program taking a look at the engine parameters before lighting up at the right time.
i used to have a tj and now have a jk so i can answer some of your questions
in cab disconnect is awesome
yes there is a bypass for the lockers, check out www.jk-forum.com
havent messed with a remote start yet but will soon, info ive found so far is wiring is pretty much the same as a magnum
drive by wire i weird and im having a hard time getting ued to it
headlight opening is about the same size as the tj, i saw something about it on the jk forum i mentiond before