Kojima honestly deserves a shit ton of flak for MGS4, like a incredible amount of flak. But a lot of other criticism for his work and writing falls flat sometimes. Yeah, sometimes the dialog is goofy and really oddly paced, yes, things do get hamfisted, but the ambitions and intentions for the narratives he creates lead to generally grounded themes and realities.
The life of a solider is tragic and most of the time unfulfilling. Murder is justified but murder no matter what leads to guilt and regret. The United States is manipulative and vicious. The digital age will lead to a abundance of information, context will potentially be lost and any one person has the tools to influence the world, positively or negatively. Patriotism and nationalism are fleeting concepts, society influences the priorities of humanity. Your own genetic history doesn't need to mean anything or be reason to do anything. Manipulation of information and the presentation of information is the best way to manipulate people.
All of these concepts and themes are part of MGS 1-3. When it comes to mainstream games I can't name another series that attempts to display themes like MGS does.