"Who knows" is about right.
I think it depends mainly on 3 things:
1. Audyssey XT32. If you think Audyssey XT32 improves the SQ in your room over Bypass (as PENG and some others),then I don't see you going over to YPAO because I don't think YPAO is as good as XT32. With Audyssey, at least I felt that Audyssey Reference and Audyssey Flat didn't sound like DSP modes. I still preferred Audyssey Bypass, but I could actually live with Audyssey Flat. There is no way I could stand YPAO Flat or Natural. They suck.
But good for me, YPAO THROUGH/BYPASS sounds awesome in my room. Otherwise, I would have returned the Yamaha.
2. Reliability. Yamaha is supposed to be more reliable than other brands. If you've had any kind of bad experience with your $7,500 Pre-pro dying after 10 years and the main authorized repair center can't fix it after 2 attempts, you just might get pissed off and order a Yamaha from Amazon to try out.
3. Price. The Denon X4400 and Yamaha A2080 are both $1600 MSRP. What if the X4400 goes on sale for $800 brand new next week and the A2080 remains $1600? I don't see too many people paying twice as much to get the A2080. But for similar price, I would get the Yamaha personally.
Bottom line, in terms of SQ, both Yamaha and Denon/Marantz can sound awesome.
But, who knows?