You might want to put a disclaimer saying barring Bethesda lore because otherwise this thread is going to get real boring, real fast. So I will just be considering 1,2 the Fallout Bible and New Vegas in my answer.
My gut reaction was the Vault Experiments, but actually disregarding Bethesda lore and just taking the West Coast games into account, they're not bad. Vault 22, Vault 11, Vault 34, Vault 19 and Vault 21 are all actually good uses of the premise, and the ""retcon"" of Vault 15 into being an experiment regarding multiculturalism is good too.
My actual answer then would be the Enclave's creation of intelligent Deathclaws. I think talking Deathclaws are massively stupid (and considering how the Fallout Bible tries to wipe them under the rug, so does the Word of God) and Navarro's experimentation would have been better served as the human kind. Or at least, human to us. Not in the eyes of the Enclave.
My change would then turn the occupants of Vault 13 into the 2nd Generation Mariposa Super Mutants. A large group that migrated and decided not to stick around in the caved-in ruins of the Enclave mines. Confused, mentally deranged, I imagine they would have been outcasted and attacked by local Wastelanders without the temperance and wisdom of the Unity Remnants. They'd be reclusive same as the Deathclaws, and request the Chosen One find them a component same as the Deathclaws. It'd add a nice dramatic irony onto Fallout 1's story and its potential "bad ending" too. Perhaps you could guide them into staying in Vault 13, or abandoning it and moving to Broken Hills.
It would also add some nice context to the combat dungeon at the Mariposa Ruins, since you could say those that stayed behind were too far gone and completely bonkers.