You're absolutely right, but then even most aftermarket set ups tend to sound quite bright.
That is why I like Pioneer so much, always sounds so much smoother than the rest.
I have an Alpine W925R in my ML at the moment, an although better than most Alpines over the last 10 years it still needs a fair amount of tweeking with the parametric EQ to tame it, and it never sounds 'smooth'.

I went with it as it is one of the only double din units with DAB and proper time alignment, which to me is one of the most important features.

I have been impressed with the Logic7/Harman/Top Hi-fi* system in the E generation of BMWs, along with the underseat subs they have given a pretty 'nice' sound for a factory system.

But the basic system in the E and S Class Mercs have also been good, helps they have 6.5" drivers in the doors so you get some fairly decent weight from them, and the tweeters never sound shrill. Just adding a nice amp to the factory set up can give some pretty good results too.

But, no matter how good you get the system, if you are having to crank it up to get over cabin noise you are fighting a loosing battle.

The cabin noise in my E350 Estate was terrible, and because of that it needed driving to the point where it sounded shrill, a real shame after the two previous generation E Class's sounded so good.

No Darling, I've had it months!