I am going to take some punishment for this, but there were a few parts I like and can live with.
Attis and his mutants looking for a cure for FEV induced sterility.
While the manual talks about Vault Tec having FEV this was never actually mentioned in the game, instead the Vault Tec scientists were doing research on fixing genetic damage caused by mutation and radiation.
Even Attis himself says this, he wasn't looking for FEV but for the means for Super Mutants to naturally reproduce.
The Vault Tec Vault.
I could actually place this in Fallout canon, Vault Tec having its own secret Vault for its employees.
Vault Tec knew what the US government/Enclave's true intentions were with the Vaults, so rather than taking shelter there or its CEOs hiding in Enclave shelters like the Poseidon Oil Rig, they instead made their own facility for themselves and selected personnel.
But Vault Tec wanted to go further than just survive, they wanted to rise like a phoenix from the ashes.
As the US government would be rebuilding the country, they would be the supplier of all high tech goods that would be demanded, taking over the position of companies like West Tek, General Atomics International, and Med Tek that surely would be wiped of the map during the nuclear exchange.
Before the War Vault Tec had been acquiring various technologies through legal and illegal means, reverse engineering their own versions of these to sell during the rebuilding. (not as if the original manufacturers would ever charge them for copyright violations)
They got power armor and energy weapons from West Tek.
They created their own line of security and service robots to compete with General Atomics International.
And after the war they started to work on medical technologies of their own as well as bio engineered weapons such Deathclaws which embryos they got through the Enclave.
They also did some work on modifying captured rad bugs (pseudo scorpions) retrieval teams had brought back from the surface.
Everything went well until Blake, the security officer went crazy, and united the other security guards behind him to take on the scientists.
The fight followed which caused the explosion that separated the Vault into independent parts, and forcing the guards to return to the surface while released samples from the laboratory and the radiation of Los turned guards that managed to survive into Ghouls.
Okay, I am going into hiding now.