Oh, well, you were warned.
I have to be brief (damn day job) but here's my comments:
Seems to me that Audyssey is flattening the hump best it can without aggravating the dip a few Hz higher. As Chris mentioned, to really see what's going on OmniMic or other dedicated measurement system would be helpful. It is possible that by moving one or both subs you could flatten the preAudyssey response and that will improve the post Audyssey predicted response and will likely sound even better. You would do what I call a "measured sub haul".
Absent a measurement system you can do this using Pro but it is not as accurate and is considerably more cumbersome and time consuming. You delete all but FR/L speakers and do minimum 3 position measurement for each possible sub placement. Once you find the best spots that are acceptable and practical in the room, you do a full rerun with all speakers and at least 10 mic positions.