Here's what I got out of the game's exposition:
The true villain is not the Patriots. The true villain is the AIs, is the System (and systems in general). I think the point is made quite clearly that the "war economy" and the idea of eventual complete SOP ubiquity weren't planned from the first, they were invented by the AIs.
Throughout the series groups go out of control: the Philosophers were formed in horrified reaction to WWI, but their system prospered on conflict and took advantage--possibly even instigated--WWII; FOX Unit was meant as a tool of democracy but was usurped by Gene and redirected to violence; FOXHOUND repeated that problem with Liquid. Finally, the Patriots were based on high morality and the ideal of a unified world, but they squabbled and their conflict (and growing technology) led to creation of the AIs and nanomachines, which provided an avenue for total fascist control of all society.
Metal Gear Solid is humanist and individualist. Throughout the series very few people are truly evil. It's the rituals and systems they create which cause evil, by ignoring the differences which define who we are as people, and squelching the humanity that should be uppermost. Ideologies--even ones born from democratic, positive principles like the Boss'--eventually run to disorder and ruin. Big-picture thinking misses the point, Kojima says over and over again. All we have is personal goals and dreams.