Easton Dark said:
"You are the chosen one"
I like just being the guy who kicks a lot of ass because I'm cooler than Fonzie x2. I don't want destiny riding me all day making sure I win.
Being "chosen" always seems like a trite replacement for actual motivation, and it usually enforces another thing I myself am starting to dislike in video games: Making the protagonist into some unstoppable, alpha-male badass. The last Spartan, a member of the SAS, or the COGs, or the Assassins, or the Dovahkiin. Unless there's some fucking awesome lore behind it, it's just... bland.
I like this aspect of Dark Souls: People often refer to you as the Chosen Undead, but the first character you meet in the game was another "Chosen Undead" who failed; lots of the characters in the game hint that you are simply the latest of many candidates, and the game very rarely makes you feel like a badass. The entire game is largely unimpressed with you.
Also in a similar vein, black and white good and evil. In Bastion, the Narrator solemnly points out that the monsters you're attacking were just animals that were scared senseless of the Calamity, among other things.
[potential spoilers]In Assassin's Creed III, the first few hours of the game are spent doing the exact same thing you'd be doing as Ezio or Altair or Desmond, and you don't question any of it until it's revealed you've been playing as a Templar the entire time; there are loads of subsequent arguments between Haythem and Connor that actually outline the ideological differences and motivations of the two factions.
[/spoilers] In Thief, you play as, well...
The point being that these are better ways to approach a conflict than whatever you're shooting at = super bad guy. That is a stale, piss-poor excuse for narrative.
I hear Spec Ops: The Line plays this trope like a fucking violin. I think I need to check it out.