I haven't seen it posted in this thread but the current thinking around the internet is that he was forced out of Konami because of the content in the game. Anyone who played MGSV: Ground Zeroes might recall it featuring a number of disturbing plot points, far beyond anything we've come to expect from the series. Since GZ was intended to introduce players to an all-round different direction, it's assumed there will be more controversial topics in the main game. It also lines up with Kojima himself saying he may have to leave the game industry because of the taboo subject matter he's tackling. Given that most video game publishers stay away from this kind of stuff, it's believed he actually may have went too far.

The latest controversy surrounds a real-life Italian doctor attempting the worlds first head-body transplant. He looks exactly like the doctor who Big Boss wakes up to in the epilogue of Ground Zeroes and beginning of the full game. He's actually written considerably on the symptoms of Phantom Pain as well, so many believe the subtitle goes beyond Jack losing his arm or his fallen comrades. The doctor claims to be oblivious to any connection to Kojima but there are a lot of weird connections here. Some people are going as far as to suggest the whole operation and all of its published medical papers and talks are a part of the largest viral marketing scam in history and that Kojima is attempting the biggest mind smurf of his career. That's a little extreme but it's becoming likely that the game's story will explore some of the issues raised by this operation and that whatever Kojima is trying to say about it, he's gone off the deep end for realsies.

Not sure if I outlined this well or not but here's some links about the situation if you guys want to read more:

http://www.kotaku.co.uk/2015/04/22/m...lid-conspiracy

http://www.neogaf.com/forum/showpost...&postcount=403