I am quite shocked that nobody (as far as I can tell or as far as I have read) has compared this game and its story arc to Star Wars. Ultimately this game is about the redemption of Big Boss and his return to good from evil. Aside from the obvious differences in setting and plot, ultimately the story makes you feel compassion for what you had perceived as the villain for the majority of the story. Also (spolier) the villain/ main character dies in the end. Is this intentional or is it just a traditional story telling vehicle? Also while some may think that the story is about the main protagonist, I feel that they represent a vessel for the viewer/ player to experience the story, in other words you are Luke Skywalker and Solid Snake.
This theory may come off as bat shit crazy, but I do think that it is worth considering and worth examining. Please do not hesitate to disagree.