There were many hints in the game without having to read a spoilers thread.
The green eye, the binocular-patch, the IA Pod and Huey saying "Jack, is that you? No..."/"Boss, is this really you?", the reflection in the chopper (your avatar's face shows up in the reflection), the fact that the real Big Boss never had any horn or missing arm, the e-cig, the fact that Eli's DNA Test came up as negative (it could mean he wasn't Liquid... or Venom Snake wasn't the real BB), the mission snake-shaped scar on his chest from PW when you select "naked" suits in the Sortie Prep screen. I might miss a few of them, but yeah, I knew it the whole time, but still loved the "Truth: The Man Who Sold the World" chapter.
Especially when I saw: "Big Boss... Benedict "Kazuhira" Miller... Revolver "Shalashaska" Ocelot... Punished "Venom" Snake"... KNEW IT. But I loved how the original intro chapter was cut to make you doubt and put the blame on the coma and possible hallucinations. (it really sounds like I'm the only one who loved the story here...)