I think the issue with a lot of Genesis music, which causes people to think it sounds bad, is that the 16-bit era saw a transition to using lots of composers who weren't necessarily adept in the sound programming department. Of course that was a thing before the 16-bit era, but I suspect that as systems began to support more channels of audio, and MIDI became standard/ popular, a lot of game developers would hire someone to write the music and then hand it off to a sound programmer. Or to use tools that made it easier for the composer to 'not worry about it'.
I think more people are cluing into the respective strengths and limitations of the Mega Drive and Super Famicom sound systems these days. The level of work Savaged Regime and others are doing should encourage more chiptune interest, too.