I will say I'll be pretty bummed if the game's biggest secret ends up being getting a kind of okay rune from the brain in the nightmare by doing the Make Contact gesture.
Well, 70% of the game is a secret per se. People can miss on a lot of optional areas and bosses if they just continue linearly.
Getting to the Upper Cathedral, getting the tonsil and finding the exact location, finding the abandoned WS, ect.
But yeah, that mother brain contact is the biggest secret though.
Shit was mindblowing when you recieved the rune.