The Paz scene music is one of the few tracks on the OST that strike me as genius. It sounds like something out of 'A Beautiful Mind', it's a really good piece of music.
But so much of the music is forgettable. I can't remember what played when I fought Sahelanthropus. I can't remember what played when I was infiltrating OKB Zero. Or fighting the Man on Fire.
The Paz music, the Skulls theme (Parasites), the main theme (or at least the core melody) and the last half of the music that plays when you escape with Huey.
And the twist, yeah, when I first saw it I saw it purely in meta terms and it wasn't that bad. I saw Big Boss, the MSX and thought "I see what Kojima's doing". Then I realized that the twist explained actual story events, like Eli's blood test, and I hated the twist for intruding on the canon.