The thing is ghouls seem to be increasingly more functional as the series progresses. In F1 they couldn't move fast because they were constantly in pain, or for that matter even wear clothes other than rags because the chaffing hurt so much. In F02 there were ghouls with armor and running, and in F3 they were pretty much stinking and ugly, but otherwise no other shortcoming. By NV even feral ghouls wore armor and sprinted faster than any human...
You had plenty of ghouls complaining of aches, pains and parts falling off. Doesn't sound pleasant.
What defines the quality of the SM generated is how much radiation they have in their systems when they mutate. Ordinary wastelanders don't usually amount to anything much higher than Harry's level, but a vault dweller for instance would always become far stronger and more intelligent after becoming a SM.
Well you have half the formula, the other half is previous exposure to FEV.
Most of the governments supply of FEV was stored at the West Tek Research Facility.[later renamed the glow] The great war wiped the surface clean and released it all into the atmosphere. The radiation neutralized the mutation properties of the virus however the people exposed to it were partially immunized to its effects. This partial immunity was past down to future generations.
So when The Master comes along to try and create his super mutant army. Those dipped in the FEV who were partially immune turned out like idiots.
This is the real core reason why a vault dweller makes a better super mutant as they wouldn't be partially immune to the effects of FEV.
This is also how how the Enclaves modified FEV virus plan works. Wastelanders and super mutants would be killed by the virus while those descendants from people sealed in vaults or similar shelters would be unaffected. This is why the abducted the citizens from Vault 13 and Arroyo. They needed a test group of pure humans[and of course they couldn't experiment on enclave citizens] and they needed a sample group of wastelanders and who better then the tribals of Arroyo who largely descendant from those who followed "The Vault Dweller" into exile from Vault 13.