I'm not his biggest fan, having read his report on the experiment he not only acted terribly unethically he also got absorbed in it himself. Its just a really bad thing for a scientist to do, and to do his work these days would almost certainly get him fired. Comparing the prison experiment to Milgrams experiments, which were controlled, safe, and repeatable, is frankly dishonest.
I appreciated the candor Zimbardo put into his book, but that candor underscores your criticisms. Milgram was far more rigorous in his controls, and in his ethics. If one were to "duplicate" Zimbardo, it would need to be done with confederates in the fashion of Milgram's experiments, and would likely boil down to being an extension of Milgram.
In March, a user on Reddit emailed psychologist Philip Zimbardo (leader of the Stanford Prison Experiment) to arrange an "IAmA" interview. Zimbardo agreed to answer the top 5 questions from this thread. Yesterday his answers were posted here.
The chosen questions touched on research ethics, what he originally expected to learn from the experiment, the role of psychoactive drugs in society, reading recommendations and more.
After responding, Zimbardo posed a question of his own to Reddit: