The stage fatality was left out of "Pit II" because it would require a lot of work to create falling animations for non-MK2 characters.

Johnny Cage was going to be the only classic character to not return. Because his actor quit/was fired after Mortal Kombat II, a new actor had to replace him, which meant remaking all of his sprites. Johnny Cage also replaces the unmasked Sub-Zero, which can be seen in early promo photos.

Due to space limitations, the N64 version of the game does not feature the unmasked MK3 version of Sub-Zero as a playable character. Instead the masked, classic ninja version of the character is altered to use his plot, ending and moveset including Ice Clone and Ice Shower.

Originally Tremor was going to be playable in Mortal Kombat Trilogy, but was ultimately replaced with Rain instead.

Within the source code is evidence of unused Treasures of Shao Khan which were to be reward options after beating the single-player mode:

• REWARD IS THE OPPORTUNITY TO WITNESS THE INNER ANIMAL ALL WARRIORS POSSESS.
• YOUR REWARD IS THE OPPORTUNITY TO WITNESS THE CHILD IN ALL OF US.
• YOUR REWARD IS THE OPPORTUNITY TO WITNESS THE KIND SPIRIT WITHIN ALL WARRIORS.

These appear to have been Finisher Demonstration compilations, dedicated to Animalities and Friendships, respectively.