If you dont use the MultiEQ app to run Audyssey, then it defaults to the midrange compensation option being on (the BBC dip). You need to go into the app and turn off midrange compensation, that alone will suck a lot of life out of the mids. I limit the correction range to about 450hz for my setup, the auto EQ works best in the modal frequency range which depends on the room but tops out around 300-500hz if memory serves me correctly. I chose a spot where the response was flat in that region, and set the limit there. As long as the crossover is well implemented, its likely that you are better off not letting Audyssey try to perfect the curve for the upper midrange and highs. It will also set your mains to large by default, so you need to go back in and make sure they are set to small and crossing at 80hz (presuming you have a sub).
You can also play with the curve, and if you want it a little hotter in some specific range, just change the audyssey curve and it will compensate accordingly. Its a pain to do on a small screen, but you have the ability to set a house curve already if desired.