I'm REALLY sick of the whole "good/bad" choice thing. Deus Ex did it perfectly: There are three different endings. None of them are inherently good or bad, but all three will change the world in a profound way, and there is no "making things go back to normal" choice. (PRIMARY VICTIM: Star Wars: Jedi Academy)
First-person cutscenes. What Half-Life did perfectly was not that your eyes never leave your head, but that you never lose control of your character. Furthermore, people's eyes don't REALLY shake that much when their character just leans a little bit to the left. If your game's cutscenes are more easily presented with a third-person camera, go for it. (PRIMARY VICTIM: Clive Barker's Jericho, but it happens to a lesser extent in other games)
Silent protagonists. Gordon Freeman was silent because everything was your choice, and you're just playing as "you". And you're named Gordon Freeman. But a game like, say, Far Cry 2, involves some very direct choices. You pretty much HAVE to do missions for diabolical warlords in over to win over their good side, and that on its own says something about your character. Besides, he makes his own statements in the loading screens.
Hiring people off the street to do your voice acting. I think the big lapse here is that actors don't really get enough of a sense of what their character is like. Be sure that voice acting actually comes later, so they can see their semi-completed character, and animations of them doing stuff. Also, fire anyone who over-exaggerates their lines.
Putting us in a setting as a soldier. I don't mind it...but I hate it when it happens too often. Which it often does. It's hard to get any sense of humanity in a game when everyone you know is experienced in killing people. No one is innocent. (PRIMARY VICTIM: Call of Duty 4. I did not feel sorry for the nuke victims whatsoever, and I am not alone.)
