For one, fusion seems to lack the bass (even with the filter turned on), of course this is due to the filter on the early M1's. TmEE's audio modded M2 is cleaner than the best M1 (the ASIC is inherantly superior to the discrete YM2612 plus there's no headphone amp to go through), though this lacks the bass as well (inless filters are added as part of the mod), but that's part of what makes it cleaner as well. I'm not sure on the CDX, though its supposedly the cleanest of any stock Genesis/MD system (albeit quieter).
In any case, in comparison to Fusion, this is just what I remember reading, others (like TmEE) could better explain this. (I think one reason would be that the YM2612's sample rate for the FM channels is 50 kHz -higher on the ASIC I beleive, so Fusion wouldn't be able to match this as it's limited to 44 kHz)
Either way, it's a bit difficult for the average person to tell the difference after a certain point. (granted a system that's not in pristine condition, particularly with a bad headphone amp or dirty volume slider on their M1, will have other issues)


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