I've set up two different room correction systems for my 2.2 channel (music only) system over the last 5 years; first a "sub-only" Velodyne set-up, and most recently the full-range Audyssey Pro 32XT in an Onkyo pre-pro. My process might be a bit more anal than some other folks', as I always run many, many set-up sweeps with each combination of gear. Since I own a sh*tload of stuff (accumulated over the years), those combos have varied quite a bit: several different subs (Velodyne, Rythmik), speakers (Maggie, Ohm, Verity, Merlin, etc), electronics (ARC, Joule, Cary, etc).
As a result, I've run many hundreds (possibly more than a thousand) sweeps over that period, and listened to the results. Obviously, some were better than others (sometimes, pretty dramatically so), but ...
Off the top of my head, I cannot think of a single instance in which the "pre-EQ" result was better than the "post-EQ" result. My room is inherently somewhat difficult, but I have made it reasonably workable with passive treatments - including various absorbtive panels and bassbuster style Hemholtz devices. It sounds borderline okay without room correction. However, for me, the improvement below 100hz has always swamped any offsetting compromise introduced by the room correction system.
Just my humble O from my experience.
Marty