The master is completely understandable if you see things from his point of view, however. Imagine that most of the world has been laid to waist by a nuclear holocaust caused by worldwide conflict, that renders the world incredibly hospitable to ordinary human life, and that you witnessed and managed to survive it after falling into a vat of phlebotium and becoming something far different from a human and noticing that everyone who is subjected to the same thing become beings that, despite flawed, are far more capable of surviving then a normal human, and some of them even retain their intelligence. With some good deal of research, you might be able to perfect the process and produce a whole new human race that can possibly become superior to humans altogheder.
Really, if I was in the master's shoes, its probably what I would attempt to do, altough I would be far less agressive and far more secretive about it untill I actualy succeeded. The only reason he didn't succeed is because the master was, quite literally, insane.
The legion's behavior also matches quite a few tribes and kingdoms of old. Its all a matter of perspective. You cant apply real, modern world ethics and morals to such things, simply because they exist in a completely different universe of ethics and morals.
You must never forget that we had far worse things in ancient history then fallout:NV's legion. The legion is basically the roman empire without the cultural and ethical achievements that actual rome had as its base, and rome was still pretty ruthless.