Bob Violence wrote:

http://www.gamespot.com/ps2/action/metalgearsolid3/news_6029469.html

Kojima declined to comment on the main theme of Metal Gear Solid 3. However, he confirmed that there will be one theme that ties the three Metal Gear Solid titles together. Kojima also noted that there will be an antiwar theme in Metal Gear Solid 3. Giving a few examples, Kojima explained that there are probably some people who do not know that a Soviet Union used to exist. Kojima also gave an example that Afghanistan is seen as an enemy by America right now, but they used to be allies 20 years ago. In addition, Kojima stated that he believes it is important to know what to protect, since history and humankind's values tend to change dramatically as time passes.

Apparently the game will be nothing less than a commentary on the transient nature of international conflict and a grand summation of the values mankind should "protect." This despite the fact that Kojima claims elsewhere in the article that the emphasis will be squarely on gameplay and not on the story. Uh-huh.