Indeed, vastly different game.
The SNES version is heavily story driven, and has plenty of dialogue and a fare amount of puzzle solving. The game is, for the most part, quite faithful to its source material, and it shows a lot of what makes the Shadowrun setting interesting, without trying to cram too much into the game. Just to save you from some grind if you decide to play this game: don't try to get everything that is sold, instead early on, as soon as you can no longer get any further in the arena, buy the most expensive pistol that you can afford. Later on, upgrade to the combat shotgun (don't bother with the other pistols, or grenades). Also boosted reflexes+shotgun>the best gun in the game (last time I played through the game, I just skipped the best gun, it was not needed).
Overall, this is, in my opinion, the better game of the two by a longshot. In fact, even though the controls feel a bit on the clunky side, this is still a darn good game.

The Mega Drive version on the other hand is a bit less linear, and offers a lot of semi-randomly generated side missions (that all start to feel rather samey after a while). The story is less interesting, and I thought controls were even clunkier than the SNES version. Overall, this game has aged rather poorly, again in my opinion.