Audyssey is great for room correction. It works great but I find that low freq LFE needs to ne turned up at least 3 db from what Audyssey sets.
One of my favorite features is Quick Select. Check if your model has it. I wanted different settings for music vs. movies. Basically, for music I use Audyssey Flat (no high freq roll off) and I lower the LFE volume. For movies I want Audyssey (high freq roll off) and I crank up LFE.
I agree pretty much with your entire post; but I just wanted to add that when I manually adjust the LFE sub out on my AVR2311-CI; I have to adjust that setting and lock it in on each of my quick selects that I want changed.