There are many threads where the discussion veered towards whether or not the game's portrayal of torture is acceptable or not.
It's not silent approval, you can find plenty of people who object to both in equal measure.
My issue with everything is this:
In past Metal Gear games the Violence was always been kind of on the goofy side, with light-ish violence. Sure the violence was there but it was always kind of silly. The torture was even silly - as the characters were usually buck naked strapped to some silly torture machine. Ocelot was essentially a sadist and a villain and not really meant to be empathized with.
I don't think you're supposed to like what you're doing in MGSV - it's supposed to be the depiction of a man becoming a horrible person... but everything in the game from what I've heard, and seen is handled FAAAAAR to casually to really represent it properly.
This game throws some really dark shit at you, because supposedly Kojima wanted to make a darker game with much deeper meaning, and gray area storytelling... but unfortunately goofiness, and darkness don't go hand in hand... and you can't tell a "mature story" and spin the tale in a "dark way" while including the ridiculously silly themes that MGS uses... It's like "You just killed a child soldier!" Fuck... I'm depressed now... "Hey boss, do you believe in Santa Claus?"
Really? See that's the inappropriateness I'm feeling from the whole thing. In GZ he deals with two kids, one is forced to have sex with other, and one child is gang raped by a group of soldiers. There is so much real life darkness, mixed with light-heartedness that the entire game feels likes it's relishing in it's sadism.
Now if you take into mind that Hideo has always tried to guilt the player about their enjoyment of murder, and horrible things that they do in these games... you get a different feeling about it. Hideo hates war, and is extremely anti-war... perhaps the goal is to make you feel uncomfortable... in sort of Japanese spec-ops kind of way. I don't know I haven't played MGSV yet, but I will... and after that I will determine how I feel. Past games have rewarded non-violent playthroughs, and in MGS4 if you kill enough people Snake vomits while he hears liquids voice saying "you relish the killing don't you?"
MGR dealt with violence, sociopathy as well as PTSD and dissociative personality disorder. Do they handle these things well? Nope, but then again Psychology is nearly non-existent in Japan.