Kojima deserves criticism concerning his project-planning and executing skills. For sure...
And I do get what people mean when they say "the story sucks", because many people consider a "story" to be something wholistic - Introduction, plot, ending, character dev., etc.
I don't want to put the man on a high pedestal here and I've surely grown out of personality cult habits...
But now when I take a distanced look at Kojima's work, I come to the following conclusion: Kojima is not a genius because he is one of the best game-designers out there -No- the man needs to credited for being a post-modern philosopher expressing himself through modern pop-culture. This may sound far fetched and "high-horse", but please take a while to think about it...
The "story" (see traditional definition) in MGS has always been all over the place, but there is something very consistent about the series: the refelction about the world and where it is heading.
MGS 1+2 featured pretty Sci-Fi driven concepts like transhumanism. With Snake Eater Kojima started to discuss ideas like patriotism and nationalism. In MGS4 he showed us a world where this ideas don't seem to matter anymore (=post-modernism). From our present perspective we might ask "why would something like this happen?"
Kojima's fails to tell a traditional story in TPP, meaning: what happens to character x and y how is a linked to b....BUT as for now MGSV closes his arch of reflection (see above):
The whole "lingua franca" concept is absolutely brilliant. The execution may not deliver, but holy fuck...there is some really deep stuff to be found here (in a video game!!!) if you are only slightly into this kind of topics. Skull Face's monologue is basically an answer to the underlying topics in MGS3 and 4 - "What defines a nation and what does it take to break it appart?"
He started with "far in the future" concepts like nanomachines and Human-AI-fusion and ended with something very tangible and relatabel - language.