I voted for Sonic 2. Imo, it's the best non-RPG of the generation. Top to bottom quality and fun. Sonic 2 is a Sonic game which really understands how to design levels which allow you to build up speed and use your momentum to discover secrets and perform cool tricks while still providing a good level of challenge. Masterpiece.
Anyway, I have to say that the Nintendo bias is getting crazy now. If Wolfenstein 3D can get a run-off and win, I would accept Sonic 2's loss, but Mario Kart? Really?? It's not even a good game. The later Mario Karts are great fun (still not GotY material), but the original on SNES is not at the same level. It really does feel like too many people will just vote for whatever Nintendo game came out that year like some kind of hive mind.