
Often times, in stories where the character who plays the villain is supposed to come as a surprise, it doesn't. It's really not surprising. It is hard to set up the board with characters who all have a place in the narrative except for one. But the best books I've ever read, and the best movies I've ever watched both have one thing in common: they employ common character archetypes to achieve the element of surprise. If the villain hides behind a mask that we all recognize and take for granted, it is easier for them to be looked over. For example, if the surprise villain poses as the: wise mentor, geeky sidekick, or comic relief character, readers are more apt to say, "Well, I already know the role of this character, so it can't be him."
Surprise!
Surprise!