Is it possible that your suspended wooden floor is causing vibrations to enter the mic? This would make Audyssey 'think' that there is more bass response than there is and dial it down as a result. If you can stand the tripod legs on some thick-ish foam rubber, that would rule that out. Better yet is a proper mic stand of course - 20 bucks from Amazon.
What does it sound like when you switch from Audyssey on to Audyssey off? Doesn't tell us much but it's interesting to hear the difference.
I've got pretty thick carpets, but vibrations are possible. This is the same setup I used to run Audyssey with the Onkyo. I used the same spots as well (at least as close as possible). With Audyssey off, it sounds much worse. I even turned off Dynamic EQ first to compare.
I'm using the mic that came with the Denon. Dynamic volume is definitely off.
I plugged my Onkyo back in to make sure I'm not just imaging the differences. The difference is pretty drastic. I keep coming back to the sub woofer volume. On my Onkyo, the subwoofer volume was set at 50%. This set my subwoofer trim to -5. All speakers measure 77db (internal test tones) with my db meter and I didn't boost the subwoofer trim to achieve this. On the Denon, 50% sets the trim to -12 and 25% sets it to -4.5. Regardless of this, the Denon is setting the speakers level at 72-73 db (internal test tones) and the sub is well below at around 66-68 db. Boosting the sub to match helps a bit, but the Denon still lacks depth, punch, and volume in comparison.
I've been going back and forth between the two to compare -- even trying to match the listening volumes with my db meter to not let volume trick me. I've been listening to Band of Horses "No One's Gonna Love You." It's a tough track because the guitars are bright and hot. With the Onkyo, the kick drum comes through clear and clean. With the Denon, it does not.
So level matching the sub to 72-73dB on the Denon doesn't fix it for you? I have always had to level match after running Audyssey, but I still think you are going to back to a "lumpy" bass response that you prefer somewhat on the old AVR, and you just aren't used to a level response. FWIW I never ended up liking a level response so I have always opted to have my subs a little hot, usually 3-5dB over the mains. I have dialed it back to that over time as well, as I used to prefer 10-12dB hot!!! I still go back to that sometimes just for a little fun!!!!