I agree with the other two posters that one of Hamlet's main flaws is his intellect, over-thinking, and general skepticism of people. His lack of trust further isolates him and only adds to his outlook that it is himagainst the world. Compounding his general distrust (even with Ophelia) and his tendency to choose philosophical isolation over open and honest discussion, is Hamlet's penchant for the dramatic. He is essentially, plotting the entire play. He delays the action because he is always rethinking (i.e. he doesn't kill Claudius while he's praying). He delays action because he's waiting for the perfect climactic moment when he can reveal his study of Claudius' crime. In this sense, his flaws are distrust, dramatization, and his self-isolation. He is like a scientist studying and manipulating the other characters' behavior in order to reveal the reasons for their behavior at the play's end.
Seeing that we are dealing with one of the most complex characters in all of literature, any answer received here must be ruminated upon, examined, and internally debated. There will not be "a right answer" here because of the complex nature of the hero. In my mind, I cannot help but feel that Hamlet's reflective and intellectual nature provides the basis for his tragic condition. Hamlet thinks, reflects, analyzes, ponders, but this also represents the source of his pain, his melancholy, and his inaction. While he is extremely intelligent and more perceptive than most in the play, it is this cerebral nature that precludes him from acting, from engagement. Given his pain ridden composition, this becomes the source of his tragedy, as he can only give articulation to his pain and is unable to do much about it. When he does engage in action, it is futile, as it does nothing to alleviate his burden and exacerbates it. The essence of this would be that few could avoid this condition. Hamlet's thought and analysis is what helps to define his positive traits, qualities that end up becoming the basis for the conditions of tragedy that best him.
Hamlet is such a complex character that it gives thought that his own complexity of thought is his flaw. However, Hamlet is also afflicted by moodiness, depression, and mania. He criticizes everything around him and finds no pleasure in his life. His inability to identify anything good in his life and his anger and degradation of women are two flaws that I identify. Hamlet's anger with his mother is projected onto Ophelia for which Hamlet ahs no remorse. Hamlet does not accept life as it is and he does not accept the boundaries in life. He manipulates and harms others by faking mental illness in a plot to seek vengeance. Only at the end of his life does he finally come to terms with life.