I really enjoy the inclusion of the silent protagonist stereotype, especially in RPGs. It allows for a sense of connectedness with the main character, an allowance to place yourself in the part of the character and take on certain "attributes" of the storyline for yourself. It can be done incredibly bad, which is humorous, but when done right, it adds an entirely new depth to the video game.
The other one is, and I agree with The Man here, the inclusion of an evil corporation. Even though I dislike the game itself, Final Fantasy VII did a good job with Shinra and, again like The Man said, the game would have been better if it focused more on Shinra's corruption than a super-human evil-doer. Evil corporation are far more believable than one super-powdered psychotic entity wreaking havoc on the world. Or multiple super-powered psychotic entities wreaking havoc on the world.