The version on the Nintendo 64 came with some grave limitations, limiting the roster from 37 to 30, leaving out characters like Kintaro, Goro and the classic versions of Raiden, Kung Lao, Jax and Kano. The secret character Chameleon was replaced with a mysterious female ninja named Khameleon, which was exclusive to the console. There were some additions to this version though, including a brand new stage, The Star Bridge and fatalities were added for Motaro and Shao Khan. This version also added the ability to watch a video showcasing every fatality, babality, friendship etc.
Everyone is always quick to mention the limitations that came with the N64 being cartridge based. Don't forget the upside to this: Load times.
With the CD-ROM versions of the game, load times create a problem for Shang Tsung. Hence the options to turn morphing off, or only to allow 2 extra characters to morph into (most that can fit into memory, I suppose) as well as the fact that you never fight against Shang Tsung in 1-player mode (IIRC).
Since the N64 has fast load times from the cartridge, Shang Tsung morphs aren't a problem. That, along with all the extra content it has, makes up for the missing characters (most of which are just dupes).
If I had to choose, I'd probably go with the N64 version.
Also, FYI, Wikipedia states that the PS version had 3 revisions. The Greatest Hits version being the last revision. If you care about having the best version in terms of bug fixes and better gameplay, then it might be worth it to go specifically for a Greatest Hits copy.
I thought that was the original plan, then I was told it was the *game* called MKT. 5th gen games are a bit tough for me to do, because I went from 4th straight to 6th.
