2 cents
FWIW, I partially agree. The Limited does ride a bit stiff. That being said, I've ridden in worse. It's is a truck based body on frame, so I tend to think it rides ok for what it is. The F-sport RX350 doesn't ride much softer then the 4runner in my opinion.
One thing you may want to check, since it seems your dealer rushed through the prep. I once took delivery of a car and the dealer left in the shipping rubber blocks in the springs. For the first few hundred miles, I kept thinking I made a terrible mistake buying the car and my back and kidney's wouldn't make it. I'm not even sure we if Toyota ships with those, but they would be easy to see if you stick your head in and look at the springs.
My 4runner rides a bit better now with 17's and AT tires kept at ~36 lbs.
I think the downside is, the truck is fairly heavy, so if you let it ride softer, it would be mushy.
Out of curiosity, what kind of car did you have previous to the 4runner?
Hope that helps,
Todd