Self-explanatory title. Anyway...

Havik's arm-eating fatality would have suited Mileena better, especially since it was already a small variation of Mileena's vacuum fatality.

Darrius' body reconstruction would have been a perfect fit for Havik, though on the other hand Darrius did benefit from having such an odd fatality, imo.

Cyber-Smoke in MK3 should have traded his "mouthful of bomb" fatality for Cyrax's self-destruct one. Being the only sentient cyborg (at the time), laughing before self-destructing would have made more sense for him.

The penguin animality could have gone to Classic Sub-Zero, Sheeva's scorpion one for Scorpion (Sheeva could have turned into an Octopus for hers), either Sektor's pterodactyl, Shang Tsung's cobra or Ermac's frog for Reptile, but then again, most of those were hilarious, especially Scorpion's penguin and Reptile's monkey.

Finally, Sub-Zero's spine rip might have made more sense for Goro. Ripping his opponent's head along with the spine and holding it with his lower hands while flexing his upper arms is something I could see him do to show off, plus imagine the impact of an already impactful creature like Goro doing that to players. It would have suited Kintaro and Motaro too.