The Enclave batch was really just to test the science out and aside from one infamous exception, all the super mutants buried alive or imprisoned in Mariposa once the Enclave had run all the tests they needed. Well, until the Chosen One came along and let them out. They were not too different from the original batch, except they weren't being trained or tinkered with, so they all came out mentally challenged. In New Vegas, they've actually teamed up with the first generation and have their own super mutant state.
Oh, and the one super mutant the Enclave kept around was Frank Horrigan... so yay for good ol' fashioned American values.
The so called Enclave batch of Super Mutants have nothing to do with Enclave experimenting on them. They are miners abducted from Redding that were used as a slave labor in Enclave excavation in ruins of Mariposa military base. As they were digging deeper in to the ruins and closer to FEV vats they started mutating little by little. Finally reaching the vats, Enclave scientist took a sample of FEV and fled. One Enclave squad was left to hold off the mutated miners as rest of the Enclave blowed up the entrance of Mariposa base thus dooming the left behind squad and sealing off the mutated miners to the base.
As what comes into the mutation by FEV, the intellegence of Super Mutant has nothing to do with the training. It depends on factors like previous exposure to the mutated airborne strain of FEV and from the radiation levels on your body. Humans that haven't been exposed to either of these become far more intellegent mutants than those who have been exposed. The miners were exposed to huge amounts of those things and so the second generation Super Mutants became far less intellegent than any of the first generation super mutants.
Where do you people come up with these "facts" like they were Enclave experimentation?