Vault 87 was out of FEV so its not possible. I agree with you and others that it has been done before. As for the mutant guy getting his hands on a Doomsday weapon... that was the story behind Van Buren. Not saying it can't be used in a future game.
I don't like the OP's idea not just because it has already been done before, its just that I can't see the Enclave, (the people so against mutants) going out of their way to make more mutants in an attempt to make another Frank like being. Would be pretty ironic if they have to go to such an extreme in order to try and save themselves. I don't even think Augustus would be for that.
How about a really smart Super Mutant messing around with Power Armour and Fallout 2 Sentry Bots. He makes himself a mech suit out of a Fallout 2 sentry bot and frankenstein in some power armour parts. Can one up that by adding stealboy tech to it. Would make one hell of a "Boss" like enemy.
Sigh. I seriously do not think you understand what a time gap is.
There are roughly 30 years from the time the Enclave appears in CW from FO2. So, yes, it is possible that a team went into 87 and snagged some FEV. That is what possible means, they could have. Did they? Would they? That would be up to writers to decide.
I am a writer, and in college I was a history minor, with emphasis on military history. As a writer, when I see a plot hole, I wonder hmm what?
For example, a 150 year time gap is not a plot hole, it is a plot pit.
And I have never looked up anything on VB, but I guess gmta. And ya, much better plot device to have ghouls or super mutants do these experiments, for what has been stated.