I REALLY think this is the root of the problem, since this particular problem is not at all isolated to this particular Lexus model or transmission and the problem only exists on cars with the drive by wire throttle.
Even the all new ES350 still has this lag in there, even though its a lot less noticable then on ours. Most cars I've driven with electronic throttles have this hesitation in varying degrees of severity.
As you guys probably know, I traded in a 2003 ES mainly because of the shifting lag, plus other annoying characteristics of this transmission. My ES350 transmission on the other hand WITH an electronic throttle, shifts like a dream from any speed, whether slow or fast, upshifts and downshifts with virtually NO shifting lag, plus the car ALWAYS picks the proper gear, without a fuss, nor any kind of driver intervention........what I'm saying is I don't have to nurse this tranny to do what a transmission is supposed to do in the first place! Suffice it to say.......I'm completely happy with this new 6 speed transmission. Today I had a car full of passengers on a 75 mile trip through city and highway, and they couldn't get over how quiet, smooth, and comfortable this car is.....without a rattle anywhere. I absolutely love this car....it's a complete joy to drive. :)