I always felt Audyssey calibration saps away the energry in the mid bass region and also adds a tad bit of brightness to the vocals, can you try direct mode to see if you like it ?
The midrange is more thin with Audyssey on.
I prefer direct mode to Audyssey any day.
If you are lacking bass it is mainly due to phase issues, try changing phase at different values, say at 0, then 90 and 180, see which setting integrates better, if there is a cancellation the bass will be lesser.
If you have a RTA Mic you can use it to check for phase cancellation at the crossover point.
If Audysey measures the wrong values for distance, you can still correct them, measure the distances and input them manually to the AVR.
There are instances for me atleast, when i measured multiple time, i keep getting different values, i do not find Audyssey to be the perfect solution, it needs manual intervention .
Probably it works better in an acoustically treated room.