What Could Have Been: The movie focuses on the health problems associated with the massive caloric intake associated with the amount of fat, sugar and carbohydrates he was eating, rather than what food scientists and dieticians primarily criticize fast (and junk) food for: being nutritionally bankrupt and full of "empty" calories.
There was a scene in the extras on the DVD that wasn't in the movie, wherein four different foods from McDonald's and some chips bought from another location were placed in jars and left to decompose. All of them showed mold and the like... except the McDonald's fries. No mold at all. The experiment only ended because the food got thrown away by accident.