@CT Phipps, the "only" thing that The Master did was figuring out that "clean" humans turn into Super Mutants. He also cherry picked those humans, for the sake of being guaranteed to have great intelligence. Even with his methods, SMs would still have intelligence level of a child and/or a mentally handicapped person, plus diverse psychological traumas. What made the West Coast SMs different was to not spam them, and being more thoughtfully chosen.
I'm not so sure of that, to be honest. The Master already had hundreds of very intelligent super mutants years before he ever got his claws on a vault. There are more hints of the Master wishing to create more creatures like himself (aka, a
Master race) than smart super mutants. He never, never actually says that his plan is to make more super mutants (it's only a mean to an end), but he mentions "a master race through unity". He's that very definition, and every living creature wants to expand and/or reproduce.
The only dumby dumb super mutants we ever witness are the random grunt door watchers, and while we know that the lack of intelligence is a common side effect, it's not a fatality since we know for a fact that the unity army had hundreds of intelligent beings, as clearly demonstrated by Broken Hills ("hundreds of mutants", as described in the vault city traveller guide), Marcus (who said that "super mutants made peace with humans decades ago". Not himself. His race as a whole), Jacob (who understands the need of production and alliances with private firms and ghouls), the Lieutenant (the most eloquent NPC of the entire game) and the Super Mutant scientist in Fallout Tactics (who has an actual, logical plan to stop the threat from the east, and who finishes her monologue with "you stand on the side of ignorance. We stand on the side of salvation".)
Plus, he already made a dipping with a vault citizen, and he witnessed the result. A creature like Harold, aka an immortal being capable of "unity" with other life species (in the case of harold, vegetal life).
Now, I'm not stating that as a fact, but just as an idea. Maybe his plan was never to make a race of super mutants, but to make a race at his image.