Improved SQ...I had this debate and demos with a local hifi dealer, and per him there are some internal part differences from a Marantz Prepro and Marantz AVR of similar prices. I would say in a blind A/B test most people would not hear any difference in a comparably priced pre/pro and AVR. Mine wasn't a blind test, I could not tell which one was playing...but I bought the Pre/pro anyway
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In a half-hearted attempt to build a 5.1 system several years ago I had a bargain basement Onkyo AVR...I will say, my new separates did sound better. Fuller, more bass, but we're talking about a $300 AVR and a $3500 separates pre/pro+amps
I only have one system, and don't intend to build another. I have a pre/pro and 3 mono blocks manning the front 3 channels and multi channel amps handling the surrounds. I prefer the heat generating amps with their own power supplies to be in a separate casing from the control electronics...the system will run cooler especially under hard usage in most cases which could extend the shelf life.