most of the things I've complained about are minor, plus I've noticed similar defects in a LS430 (60k) and a Benz C class (50K.. I think.) With a little felt tape I got rid off the one noise I had. The engine tranny combo is peeerrrrfect. At this point my brakes have a judder at high speeds, which the dealer is going to look at, and I've heard about a possible recall.
I have a ex-l 4cyl man., so maybe by engine/tranny combo avoided many of the probs.
No doubt that both the assembly techs and the processes get more refined as time goes on. Plus engineering will make small changes to get rid of "problems" both by design and assembly techniques.
My car is very nice, but I bet the 2004's will be more refined. I would not have had to chase down the squeak most likely.