A barebones SNES vs a barebones genesis really comes down to 2 things - the SNES sound chip could handle samples far better then the genesis and it also output to a larger number of sound channels. The Genesis had better straight up synth but shittier samples, music sounded lower quality but punchier most times and by the mid 90's most developers were using more sampling so the longer the generation went the worse the genesis sounded.
Not really that simple and you got a few things wrong. First, the Genesis does have a larger amount of total sound channels than the SNES does. 6 FM channels and 4 PSG ones amounts to a total of 10, versus the 8 available on the SNES. Though in practice it was mostly 9, because you had to disable one PSG pulse channel to enable additional functionality in the noise channel which was often used for SFX. In addition to that, the one FM channel used for PCM sample playback could also be software mixed as Krejlooc mentioned, so that essentially gave it 1 extra channel for samples, and in a few cases even more (Toy Story uses software mixing to play full 4 channel .mod music during cutscenes). It is true that not every game used all the available channels, in particular a lot of western games seemed content to stick with just the 6 FM channels. But then this also applies to the SNES and not everyone fully utilized all 8 channels.
Second, about the samples. The fact that a lot of games had generally garbled playback was not because of some inherent limitation of the system. The samples themselves were fine, it was rather the programming of the sound drivers that was lacking and resulted in timing issues. It's strange the way this is brought up in discussions when there are plenty of Genesis games, some of them quite popular like Earthworm Jim or anything Tommy Tallarico worked on, which had very clear sample playback and used them quite extensively in Tallarico's case. Matt Furniss is another one who worked on a lot of games and had very good sample quality.
A great demonstration of this is Street Fighter 2 CE which was recently hacked and had its sound driver reprogrammed to fix the sample playback issues.
http://www.youtube.com/watch?v=-iE5GJNkOqs
And it should be mentioned that since SNES relied almost exclusively on samples (save for a noise generator which was sometimes used for SFX, particularly Square relied on it a lot), the 64kb RAM limit was a great bottleneck and caused many problems and limitations of its own. If we take Earthworm Jim as an example once again, one of the reasons the SNES version is missing a bunch of sound effects is because both SFX and music instruments are samples they both occupy a lot of memory. The synthesized Genesis instruments are just a few lines of code, so there is more space available for SFX samples to occupy.
This also makes it very unlikely that the full range of sound effects in Sonic the Hedgehog could be faithfully replicated on the SNES. If you relied on recorded samples for sounds like the cash register on the score tally, or losing rings, or springboards, etc, it would just take up too much memory. Instead you would have to use very short simple oscillator samples, or just make use of the instrument samples as was standard, to design the sound effects as some kind of wavetable synthesis. But this is far from as flexible as doing it with FM.
There was also another particular sound problem on the SNES which is rarely brought up by the general public, and that's the rampant issues with out of tune music. I think this is mostly caused by improperly looped samples. If they loop too fast it's going to shift in frequency after the attack/transient of the sound. SNES samples are stored in a 9-bit ADPCM format in order to compress them, but this also incurs some particular limitations in how samples can be looped (not an expert here but it has something to do with the 16 to 9-bit conversion), so this is likely one of the major culprits causing this when composers couldn't set loop data at any sample point they wanted.
The pre-Super ports of Street Fighter 2 on the SNES are some of the worst examples of this where some of the instruments are clearly more than a quartertone out of tune. Frankly I find it unlistenable.
I've found it kind of ironic that while in general people seem to regard the SNES as sounding better, but the more musically trained you are the less you end up liking it.
