According to Ed Boon, Warner Bros. suggested Neo from The Matrix as a guest character for the game but the idea was turned down because the character didn't fit in a game like Mortal Kombat.

"It was more like 'We’d love to do a guest character, who’s available?' And then we would see a list of 10, 15 characters. I remember they brought up Neo. So there were a whole bunch of ones that for business reasons or that creatively we didn’t think they’d fit."
Contributed by ZpaceJ0ck0