I finally played the SNES console version today and the biggest difference in gameplay I saw was between the goalies. The goalies act in different ways in each version.
In the SNES version, I couldn't do the move across the front of the net as easily because the goalies don't really fall down, but I could still score doing it.
I also noticed that it's way easier to deke in the SNES version. In the Genesis version, it is soo hard (at least for me) to deke the goalie out and score. My friend did it at ease with the SNES version. If he got on a breakaway, he scored (unless I switched to manual goalie).
That brings me to the next thing, which is manual goalie. I found it to be clunky in the SNES version, I couldn't control my goalie nearly as well.
Lastly I just found the SNES version to be a little choppier. Overall I obviously like the Genesis version better, but I see how people can like the SNES version because of the ability to deke.
EDIT: I also want to add that I did not see any differences between goalies with high or low stats. All goalies seemed to be equally easy to score on.