Nice looking room!
1) Definitely should have speakers set to small (but Pogre makes a point about your sub possibly being especially inept)!
2) Leave Audyssey Dynamic EQ on, but turn Dynamic Volume off! As a simplified explanation, Dynamic EQ increases the bass to mid-range balance as you reduce the volume so you still get a full sound at low listening levels. Dynamic Volume compresses the audio signal, so the difference between a loud and soft sound is reduced this is not something you would usually want for home listening (it is a common and more useful feature in many cars where road noise would cover up quiet sections, but if you turn up the volume, the sound would blast you out of the car when it got loud. Classical music is the most common example of wide dynamics between quiet and loud - much of modern music is created/mixed with the idea that the listener is using earbuds where there might be a fair amount of background noise. Exeriment for yourself, but most agree that Dynamic Volume should be avoided!
3) That glass coffee table positioned midway from the mains is really setting off my OCD. If it really needs to stay, consider putting a small rug on top of it (Austin Powers voice on) - "Shag, baby!" But seriously, at least consider putting some throw pillows on you sofa and moving them to parts of the coffee table (ideally where the reflection point from your mains are) that you are not using when you are listening. Anything you can do to absorb or scatter sound-waves reflecting off of that glass surface will help. Re-run Audyssey with the pillows on the table.
You might do a test to understand why it matters so much - simply listen with, then set the glass aside and listen again. Ideally, you would run Audyssey for both situations, but for a general "quick and dirty" test, run Pure Direct! What is happening is all high frequency (and much mid) gets reflected to your ears arriving microseconds after the direct signal from the speakers. The timing is close enough that your brain does not recognize it as a reflections (as it would a reflection off of the ceiling) instead, the attacks and releases of sounds are being "smeared" over that extra time, (perceptually) reducing the level of detail that your speakers are capable of!
