The game is FULL of foreshadowing, and it still caught people off guard, causing them to complain about it coming out of nowhere. Meanwhile others figured it out like a week after the first trailer.

• Venom's eye colour is different
• Venom vapes while BB states that he prefers real cigars in Peace Walker, even stating that the original is always better
• Eli's DNA doesn't match Venom's, despite him clearly being Liquid Snake
• The Boss' AI literally states "you're not Snake"
• Ishmael has the same voice actor as Venom, literally states "you're talking to yourself"
• Venom Snake doesn't know Russian while BB is fluent in it
• Multiple references to and uses of David Bowie's 'The Man Who Sold The World', which is a song about a doppleganger (double foreshadow since its a COVER)
• Big Boss doesn't have a sense of smell in MGS3 but Venom does (I admit that's a pretty hardcore detail)
• Ocelot constantly reminds Venom of info that BB should already know to reinforce the brainwashing

If you didn't at least suspect something was up, you just weren't paying attention.