I'm unbiased, so I feel my opinion is solid.
Things SNES version is better at:
Passing
Goalie animation and control
Controller
Things SEGA version is better at:
Speed
Gameplay
Slapshots
Overall hockey "feel"
Fun factor
I'm a SNES guy, as I was only allowed one system as a kid and picked SNES. Back then, you coundn't just pick up a Genesis for 20 bucks like you can now, so I had to make a choice. I am going to buy myself a Genesis as well as Nhl94 used for a dirty cheap price. I don't like the Genesis controller, but the gameplay is so solid I'll learn to live with it. Nhl94 on SNES appears to be in slow motion, and the skaters move like they're in quicksand. It's sad to see, but I'm able to put aside my SNES "loyalty" to show love to the ideal Nhl94, which is the SEGA version. Man is the SNES version slow now! I always thought the SNES was the more advanced system. Sad day for SNES fans, but it ain't even close!