I personally think, both were stupid broken and both are different games, the PSX had MK2/MK1 chars with broken damage output, and a far worse shang tsung morph, but the physics in that game are much similar to UMK3, while the PC version is also faster.
The N64 version doesn't have MK1/MK2 classic chars, but you have scorpion/Ermac/Smoke having multi tele combos, noob throwing shadow toss and a disabler right after making one of the most broken setups in the game, his teleport loop is much easier to do in N64 version, Super Sub-Zero with Ice Clone that doesn't freeze if you are coming from the air holding block, which he can use this to ground freeze and make an unblockable setup.
Both are different games in general, even from a gameplay perspective, i just wish he had a definitive version that could combine both games, while i love the classic inclusion of PSX, the gameplay of N64 it's something i didn't know i wanted until i tried, loved how some of the things were completely different in that game.