Hey KRIKzz. I think trying to find the "perfect" solution to the audio issues might be an unachievable feat. Without Oscilliscope readings and hard factual numbers to back up each opinion, there really isn't any "right" one. EVERYBODY has different hearing. As we age, our hearing changes. What we heard 20 years ago will not sound the same today. This is fact. Throw in differences due to genetics, exposure to loud noises, etc. and it can drive you crazy.
I'm wondering if it would be possible, once things like I/O errors and other functionality bugs are squashed, if it would be possible to have a "core" OS that folks who aren't as picky or specific or technically advanced could download and use right away? In addition, have a website where folks can choose specific mappers they want to use, specific volume level versions of the mappers, etc. etc. and customize it however their ears desire, then have it compile the custom OS for them to use?
Something similar to the SD2SNES menu creator. This could save you some hassle due to the subjective nature of audio. Of course, it would all depend on whether that's even feasible. Just some ideas being thrown at the wall to see what can stick. :p