I've owned my '06 prerunner/TRDsport for a week now and while I don't have any shudder or vibrations, the computer sure seems to hunt for the correct gear quite often. I feel it upshifts too soon unless you give it more throttle than you should for normal accelerating from a light and when you let off the throttle, at times it will "hold it in gear" while trying to coast up to a stop light(this is with it D, not 4) GMs will instantly shift to OD or "neautral" when you let off the gas. Also, the shifts are so soft, its almost like it's slipping. In a former life, I was an ASE master tech& GM master tech and while I feel this truck is overall far superior to GMs weak offerings, I think toyota has a ways to go to match GMs flash programming for the drivetrain.
P.S. This really grinds on me about all newer cars-WTF happened to the trans dipstick? are we all too dumb to read it correctly? Do we all put the wrong stuff down the tube? Looking at the dipstick was how I used to gauge when to change the fluid- no more.