"Your Princess is in another castle" - Let's be honest, this still goes on to this day. You really think you were going to kill the guy you've been hunting or rescue the damsel in distress only 4-5 hours in? Think again. I still see missions/levels that go "*insert antagonist who is the target or damsel in distress here* is in *insert random, exotic country here*. Let's go get him/her! There's no way he/she will get away." only to have him escape at the end and lead you on some wild goose chase for about another 5-10 hours, there may be another mission similar to this later on. The problem is they're almost always really predictable, to the point that it makes the entire level feel pointless.
The person who employed you, or your best friend betrays you - So overused, and again, really predictable. They try to be subtle and clever with this one, but as soon as the character you're playing as or the protagonist's confidante says something along the lines of: "Something doesn't feel right about this" you pretty much know what's coming.
One of the final missions being a vehicle section - I assume they do this to get an epic feel or have it as the climax. While what they're going for may be great, it almost always leads it to failure. This is probably due to the game having a section whose gameplay differs completely from the rest of the game, making it prone to being clunky, or sometimes flat-out broken.
That's all I got right now.