I'm really not trying to hate on the game or anything but seriously almost every plot twist in MGS4 had me facepalming the whole time. I'm gonna mention only 3 to save time.
1: The Patriots are MGS3 cast.
2: It was all the Nanomachines fault sigh ...
3: Big Boss lives *Barf*
There is a lot of games with dumb plot twists (like MW2 most recently) but MGS4 sticks in my head the most. MGS2-3 had it right.