3. Your Custom Avatar Is Reflected In The Chopper Window
This one's incredibly subtle and you basically need to squint to even notice it, but back in the ACC after a mission, if you zoom in at the chopper window, you'll see a reflection not of Big Boss but of the avatar you created at the start of the game, which is widely speculated to come into play in the online component of the game. Given how many thought the avatar creation was a peculiar way to the start the game considering how it actually isn't used at all, it seems that Kojima wasn't just screwing with the fans, and it will have some significance later down the line.