I much prefer the Genesis Shadowrun for the sheer depth of the game. The matrix could have been a whole game in itself. The first few times I played through it I pretty much avoided the matrix, but once I started getting into it, updated my deck, and started taking on corporate runs, I was hooked. It's great the way you can hack into a corporation and disable things like their security cameras and door locks, and then sneak in to complete your mission undetected. Or just hack in and steal information and then sell it off to a fixer.
Add to that a throughly detailed magic system, well-written dialogue even for the minor characters, completely non-linear gameplay, and actual shadowruns you can take on from any number of Johnsons in the game, and the end result is one of my favorite games ever.
The SNES version had a more involving storyline and a much bigger world to play in, but it lacked that extra bit of depth that I was so used to in the Genesis version. So to me it was a disappointment, though I can still see why others might enjoy it more. It's like comparing apples and oranges. Both are good in different ways.