The actual execution was a mess, but Skullface's inspiration for his parasite weapon being the experience of linguistic imperialism as a child was a really novel premise. The idea that he would get his revenge by creating a weapon that killed anyone who spoke English is some cool super-villain shit I don't think I've ever encountered before. "Race-selective" weapons, genetic-targetting weapons, religious indoctrination viruses, I've seen all those, but I think MGSV is the only time I've encountered a weapon that targets a language community.
Kojima has definitely read Lenin. He lionises Che Guevara and there's absolutely no way he hasn't looked into Che's influences. He also regularly recommends incredibly obscure Mao-era movies to people on twitter that I literally can not find anywhere, they are probably so rare that only an obsessive film person like him can possibly collect them.
The issue with Kojima is that he's such a movie fan that he's a fan of hollywood and what it produces. This love of hollywood aesthetic and style influences and americanises all of his work.