Admittedly, I am a bit late to the party. I have only recently completed the first three entries in the Metal Gear Solid franchise. My biggest aversion mainly came from the fact that the series ostensibly seemed too much like something Tom Clancy would write. Add to this the fanboy sentiments so lavishly bestowed and you have a recipe for something that is most likely going to be incredibly generic. I have to say, I was pleasantly surprised when I gave it a chance.
Each game tends to dwell primarily on one theme. In the first game, the main point is the exploration of nature versus nurture, Sons of Liberty focuses on the transmission and control of information through social means, and Snake Eater is about cultural relativism. Philosophically, these topics offer a wide range of commentary. However, they are explained at length within the game and elsewhere. Instead, the most interesting and least expounded upon aspect that I noticed was the existential journey of Raiden in Sons of Liberty; more specifically, how this journey relates to the writings of Jean-Paul Sartre.