Clearly, your profile is impressive however there is obviously some component of your application that is weak. I recommend that you have your essays reviewed by someone who has been accepted to a top program and ask for honest feedback. Make sure that you have thoroughly answered the questions and have also provided some insight into your personality and character. Also, make sure your letters of recommendation are written by individuals who can discuss your achievements and goals in detail. The content of the letter is more important than the job title of the person writing it. You mentioned that your extracurriculars are weak. Make sure that there is something in your application that demonstrates you are a well-rounded individual who is comfortable in a variety of settings. Finally, make sure your applications are tailored to each program. Many applicants make the mistake of writing one set of essays and using them for all applications. This is a bad approach and will yield negative results.