Go into things like your eq settings et al. I have my subwoofer level set quite high, because my room swallows bass. It also helps to look at your low-mids, as this is where a lot the "warmth" of your audio comes from.
Q1: what are your crossover settings/bass management with your subwoofer? Tweaking this setting can go a long way to restoring lost timbre. Play with the dialed in settings from Audyssey and Dynamic EQ, since they're not foolproof.
Q2 &Q3: I'm going to answer both of these at once so pay close...