Sure, some of their methods are questionable,
Haha, that's a funny way to describe slaughtering hundreds of innocent civilians, because they didn't have the luck to get into a vault. Which is technically the Enclave's fault anyway, considering the Enclave made the vault's, so it was there decision whether or not to make room for more people. So their murdering people, because they were too lazy to either, create more vaults, or allow extra population into some of the vaults.
Basically; Murder + Innocent Civilian = Naughty Naughty.
By the way some of you Pro-Enclavists are preaching, it sounds like you'd think it's all right and good, if someone walked outside, shot a man in the face, and when he was arrested, said to the officer, "He had radiation in his system, so it's not like it's illegal, or unethical or anything".
To the OP, the Enclave are not completely evil, their goal is very just, and is what all of the wasteland would want, but there means of achieving these goals are horrific.