Even though there have been plenty of great video game villains throughout the years, for the most part they've been pretty cut and dry. When they're not huge aliens (with conveniently placed weak spots), they're moustache-twirling baddies who love to taunt the player over tens of hours. That's not a bad thing either; we love them for it, and they make the times when a video game does have a surprising character who isn't obviously the villain at first all the more interesting.
Also, it's simply more difficult to craft a great villain twist in this medium than it is in, say, a movie, because of how many more hours the writers need to keep the audience in the dark for. They need to ensure there's enough teases and hints in there that the eventual reveal makes sense and doesn't simply feel cheap and shoehorned in, but doing that over 10-plus hours inevitably runs the risk of giving the game away far too early.
Of course, there have been some spectacular titles that have pulled this off effortlessly. It takes a lot of work to execute properly, but when a release gets a villain twist just right, it can instantly make them one of the medium's most memorable.