Johnny Cage is the only character that has new sprites. There was a reason. Midway fired Daniel Pesina(who did Johnny Cage & the Ninjas in MK & MK II)because he dressed up as Johnny Cage to advertise an arcade game called Blood Storm, which turned out to be a emphatic flop among fighting game fans. So Chris Alexander did the sprites instead.
On February 28, 1997, Mortal Kombat Trilogy was put on the infamous German index by the BPjS. For more information about what this means and to see a list of games sharing the same fate, take a look here: BPjS/BPjM indexed games.
There were several differences in the amount of secret/selectable characters in the Playstation and Nintendo 64 version.
The Playstation version allowed players to choose the bosses from the series: Goro, Kintaro, Motaro and Shao Kahn. The Playstation version also gave players a male version of Chameleon, as well as older versions of existing characters (MKII Kung Lao, MKII Jax, MKI Kano, MKI Rayden).
The Nintendo 64 version only had Motaro and Shao Kahn available, but also a female version of Chameleon, named Khameleon.