Long and short? Completely different games. The Genesis version is a top-down semi-sandbox with a very loost plot structure similar to what you find in Morrowing - it's technically there, if you want to follow it but the game also will supply you pretty much inexhaustable sidequests to explore and run in. The big downside is that the game is old school - you start with 200 nuyen, a pistol and a crappy cyberdeck; you end up grinding for cash and karma almost from the word go and once you start hiring runners you have to grind for their stats and gear too. The graphics are functional but the designers did a very good job of working the Shadowrun flavor into the text, and some of the runners you can hire are pure gold.
The SNES version is more a traditional console RPG with a three-quarters perspective and passing fair graphics: they do the job at least and are well animated even if a bit small. The game has a reasonably strong shadowrun-style plot right down to your standard doublecross but with more limited exploration: the interface is a bit . . . unique: d-pad moves the character until you press one of the face buttons which will bring up the interact (hand) or shoot (crosshairs) cursor which you then control with the d-pad while your character is stationary. Kinda feels like it was meant to be played with a mouse, actually. It also has a fairly sophisticated (for the time) dialogue system - when you talk to NPC's they will mention keywords which you can then ask them or other NPC's about, getting more keywords unlocking more dialgoue/events, etc. The SNES game also plays much looser with cannon - stats don't top out at 6 and the main character can get both cyberaugments and magic without any fear of essence loss.
Both are fun. The genesis version takes longer to get into but is argueably more immersive. The SNES version is unique and ahead of it's time in some ways, really retrograde in others but manages to tell a compelling story despite its flaws. Both are definitely worth playing. That and it's the only shadowrun videogame I know of where you can attend a Maria Mecurial concert.