As much as I don't want to bring this damn thing up again... Mass Effect. The ending, namely. It could have been such a fantastic moment, so many variables coming together to form an amazingly complex, satisfying variety of endings. Nope. Press the button, then the thing happens. Three colors, people.
OK, something that hasn't been a major controversy on the internet and we're all sick of hearing about... Erm... Far Cry 3. It could've so easily turned into something after the spirit of Heart of Darkness: A regular person thrust into a harsh environment, slowly turning insane as the artificial bounds of civilization crumble and he has to become precisely what he originally set out to survive against... Instead, we got an, admittedly pretty good, "gotta go save my friends" type story. Sure, there were a couple arbitrary nods to the whole Heart of Darkness angle, but it really wasn't emphasized at all, and it all just felt token. I just think that what Spec Ops: The Line did could have been done even better, this being an open world scenario where, if you're fighting people, it's mostly your own choice, piling the guilt on you as a player rather than the game designers forcing you into combat and then putting the guilt on you.
Also, I guess Dragon Age 2. "Hey, we're going to introduce a new type of storytelling games haven't really done before: Instead of focusing on an overarching plot, you're going to experience the story of a place, the city of Kirkwall: the different political struggles, how society evolves over time and reacts to changes, and how changes in one sector of city life affect others. We're also going to have you play a character doing rather banal things for most of the time, and chain you down to their uninteresting little story involving them doing fuck all most of the time and occasionally stumbling into tidbits of the city's evolution".
To be fair, it's a bit hard to blame BioWare for it: If you're making an RPG (which they kind of but not really were, but that's beside the point), you need to follow a single character, since you need to keep your stats and loot and all that goodness. This doesn't really mesh well with having the emphasis of your game be the evolution of an entire city. Perhaps it would've been better as an honest-to-God hack'n'slash (which it was approaching anyway), and made you play as different people at different times.