Before adding the Audyssey vs YPAO factor into the equation, first decide which amp sound you like better. It will depend on the kind of speakers you'll be using, plus your personal preferences about the over-all sound.
Personally, my preference goes to the Yamaha sound.
If you like Denon's sound, then go for it, because the consensus is that Audyssey is the best EQ system. If you prefer the Yamaha sound, then you must choose Yamaha even if YPAO, while also very good, is still slightly inferior to Audyssey. That's because your choice should be determined by the sound signature of the amp, not by the performance of the EQ.
Parametric EQ is a great thing, but it still has its limitations. It still isn't a magic bullet that can instantly cure any room deficiency.
Don't worry too much about it. Both are very good receivers, and you won't go wrong either way.
What you should be worried about is Denon's after-sales service reliability. In this neck of the woods, Denon service is terrible. Browse around for Denon service complaints.
Instead of Denon, why not try out the Onkyos. Good amp, Audyssey EQ, plus great after-sales service. Just make sure the unit has enough free space around it so that the internal cooling fan can do its job well.