If in discussing the "top three issues," the question is seeking to examine the three most profound implications to come out of the film, I think that the social and physical impact of fast food ingestion has to top the list. The preponderance of fast food in American society has to be one of the largest issues to come out of the film. When Spurlock starts his quest, he does not fail to mention how many McDonald's restaurants are near his home. In this, the issue arises that the accessibility of such food establishments makes the unhealthy consumption of food all the more easy given their proximity and easy access. At some level, I think that this begs the question for external monitoring of such a situation. While it might be business and commercial based, there is a public health issue when so many of the same type of restaurants are in proximity to one another.
Another issue that comes out of the film would be the intense effects of the "Supersized" diet on Spurlock. The physical and physiological transformation is fairly horrific. It represents the end to which a fast food diet can alter the human body composition. This is an issue that cannot be denied. Even if one wants to claim that Spurlock's methodology or findings are not entirely accurate, there is a definite claim that fast food can impact the human body in a negative way. Given the easy access of so many fast food restaurants, this is a powerful statement.
Finally, I think that the issue that is most interesting to me would be Spurlock's "detox diet." The implication of this would be that the only way for Spurlock to overcome his thirty day ingestion of McDonald's food it through total detoxification. This is a very powerful element in seeking to understand the effect of fast food on the human body. I think that focusing exposition, the execution, and the resolution to Spurlock's experiment in the film is of vital importance and represents some of the most important issues in the film.