A lot of the arguments I hear are about how nothing makes sense. Which is why I always bring that up. Things do make sense but there are always little details that can be missed in the storytelling. I happen to think Kojima is a fantastic story writer for these games. Just something about it I can't really pinpoint for you. I never had an issue with the story in these games and always felt it was good.
That was what I was referring to earlier. It does make sense to some people, but to others the plot is chaotic. It can be especially confusing to those who don't understand that their are multiple "Snakes" and what their context with each other. For any particular game, it can be difficult to figure out who the good and bad guys are because Kojima likes to have them change sides regularly. Take MGS5 for example. Big Boss is portrayed as the protagonist, but in reality he is just as bad as the rest because he is trying to build power for selfish reasons. Perhaps that moral ambiguity is what makes MGS so good, but its still confusing. These things don't detract from the overall quality of the franchise, but they can create a situation where some gamers become alienated because they didn't bother to study up before playing the games. That is what I and some others are referring to when we talk about the plot, and is a legitimate strike against Kojima. You aren't wrong, but neither are you right if we keep things in context.
I know as a fan who is really into some things, it can be easy to slip into a sort of snob attitude where we can't understand why people don't get it. Anachronox was such a game for me, but many didn't like it. Some content just sings to us. I'm really glad MGS sings to you.
All that said, MGS5 does deserve massive props. Gameplay wise, it is about as good of MGS as I've ever seen. I'm gonna put in another few hours this evening.