Skull Face's ending is perfect, IMO. A recurring theme in the game is the restlessness you feel when you've had your revenge but you still feel unfulfilled. It's one of the many forms that "phantom pain" takes in the game. Skull Face's unceremonious death lacks a certain drama and works better for it. They quietly leave him to suffer, since that's how they want to imagine him forever suffering. They don't even give him the decency of a mercy killing. But then Huey steps in and, being the spineless lil' shit he is, kicks a man while he's down. If it had been Big Boss trapped under the girder, Huey would've done the same thing.
Either way, the end result is the same for the Diamond Dogs. They've achieved peace in the sense that the threat is gone, but they have not achieved personal peace. Far from it. Instead they have a perpetual state of unease, with paranoia and witch-hunts, punctuated by the occasional tragedy. I see Ch. 2 as a short story collection of life at Mother Base after Skull Face is gone and they no longer have a "face" to focus their anger. Ch. 2 is the life Venom achieved for himself after Skull Face and prior to learning the "truth" and the folly of his entire struggle.
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