Brother None said:
FEV was based on the PIV-project, a project looking for immunity to bio-chemical warfare. The mutations were an unintended side-effect, FEV was never a mutagenic project. PIV was also a military project, consigned to Mariposa.
Well ... no, sorry.
FEV started as the The Pan-Immunity Virion Project (PVP) in a private contractor, West Tek.
During testing they noticed abnormal growth rate accompanied by increased brain activity in the test subjects so the military decided to take control over the project, build Mariposa Base to house the (now named) FEV project and started to experiment on volunteer subjects, West Tek did retain their PVP/FEV Vats.
Then the nukes were launched, West Tek Vats were hit by the nukes and the FEV contained there evaporated, mutated and became airborne infecting everything on the surface but its mutation made it mostly "harmless".
Then you have FO1 events were it shown what the mutated FEV screwed up with the pure FEV by making the Super Mutants dumber, that was the reason why The Master was looking for "pure" humans.
Now forwarding to FO2, the Enclave manages to retrieve FEV samples from Mariposa Base ruins and starts some FEV related projects.
One was using it on Deathclaws to create Super Soldiers that would not question orders, it failed (well it worked too well since they became too intelligent and decided to run away).
Another was creating a toxin agent that would kill all the tainted humans, that is why they kidnapped the Chosen Tribe and Vault 15 dwellers.
Considering the xenophobic nature of the Enclave ... the fact they did not have any Super Human project around is telling, in fact they retain that nature in FO3 so I am not seeing doing what Bethsoft SAYS they did, if Vault 86 was a control population for another toxin that for some reason backfired into turning then into Super Mutants it would be one things, another is having a FEV project around with just a different name.