Yeah it kinda went overboard. I loved the concept of language, but parasites that can be genetically modified at will to give all kinds of super powers, parasites that can understand precisely languages and kill the host if spoken, or how the dead are re-animated in fire by psychic powers because they "sensed" someone's presence was too far fetched even for an MGS game.
Also all these plus the new Metal Gear were far more advanced technologies than anything that appeared in the games that took place in the future.
I am not fully decided on what to think about those absurdities myself. The MGS series is unquestionably filled with completely inplausible pseudo-sci-fi such as the ones you mention, but not being realistic is not intrinsically a problem.
Surrealism is a valid choice of style. Sure, mixing surrealism with hi-tech military fiction is a rare thematic choice. War and politics usually are associated with a down to earth and scientific/historical view of the world. While fantasy and the more "magical" fiction usually threads on topics of more personal human experiance such as psychology, emotions and interpesonal relationships.
What kojima tries to do though, is use a mix of militaristic light sci-fi, with anime-like sci-fantasy to delve into larger overarching political philosophy. It is a very unusual mix, but that does not mean it has to be bad. The question is, does he solve the incongruencies that this weird combination leads to. My opinion is: not entirely.
I really don't understand why he feels the need to over-explain the logistics of every single device and technology of his universe if it is such a balls to the wall bizarro land universe with human vampires and floating fortune teller goths. Am I supposed to suspend my disbelief or not? Because I try to, but then kojima seems to WANT me to scrutinize the complete absurdity of the ellements of the world he creates by bothering to explain why those things are possible. He creates a universe that requires one to lower their pedanticness, but then choses to be pedantic itself and invites you to partake on it. Why? What for?
As if any half brained person reading a couple books about military tech or whatever can't hand wave at genetic mutation this and nano particles that and come up with a plausible enough explanation for anything imaginable as long as you accept a sprinkle of technical lingo as enough evidence for feasibility. There is nothing intelligent about it, its just tedious.
The political philosophy he brings about is deeper that what you see in most games, and I wouldn't complain if he didn't rub it in our face and spelled his moral lesson out multiple times over in every game. They are not completely original or sophiaticated ideas, and they wouldn't have to be, if the delivery was more subtle and humble, but the guy overdoes way too much in every game.
The aesthetics are very striking, but verge on camp, and pop-culture parody.
The gameplay is very fowardlooking in many ways, but it also always has it's share of oversights and clunk.
So that's why it's so easy to hate on his creations. There is a lot to love in them. But it seems for every brilliant idea they carry, the game purposefully works out ways to undermine it. It's like kojima wants to shit on his own work for some reason.