Here's where I think you missed the point of TPP. The character you want the game to be about, Big Boss, it isn't. It's a character driven story about a guy's descent into madness due to his idol, in this case BB, using him for his own gains. He was forced to live the legend, and build up the name of Big Boss all while the real deal was off setting up his Army without a Nation.
Then when the unthinkable happened and Venom had to save the world by murdering all the Diamond Dogs, Big Boss needed to control his monster and take him out, sending his two best recruits Grey Fox and Solid Snake. The entire story is about what a dick BB is, and how Venom was a victim. Think of it like Frankenstein and his monster.
Again, all the hate will come from people who wanted this game to be Big Boss' final ride, instead of the conclusion to the saga that finally links the old and new games together.
tl;dr - People are going to be pissed because TPP isn't the game they want it to be.