The N64 version takes advantage of the hardware's anti-aliasing (it blends pixels when an image is seen up close so as to prevent the "blocky effect") Also, since it's stored on a 16MB cartridge (unlike MK Trilogy, which was on a 12MB cartridge), ALL the sounds from the arcade version are included and in high quality.  Plus, the Rumble Pak is supported (so that you can feel everything from the snap of a Fatality to an explosion in an Ending), as well as the Controller Memory Pak (used to save controller configurations, High Win Streaks, etc.)