I want to just put it out here, that whilst I agree that cutscenes whilst brilliant aren't the ultimate true method of game storytelling and that Half Life tells a good story through new techniques,
one method they use is TERRIBLE and that's the one people mistake for the good one.
I'm talking about the "having a cutscene happen near your player" that Half Life does, and is then copied by games like Assassins Creed. Closely related by people just talking over a radio whilst you play.
It does nothing, it breaks immersion because you're character is no longer reacting to the world realistically, instead of participating, like they do in a cutscene, you're character becomes a moron, wandering round the lab instead of facing the scientist talking to them. The player has no control, he has to listen to the cutscene, yet making him think he does. Either this leads to distracted wandering around whilst the talking happens, which detracts from the story, or the player stands still and watches. IE it's a cutscene but a really bad one from an awful angle.
What half life did right is environmental story-telling. Copied by Bioshock. Bioshock's story is infinitely better than Assassins Creed in presentation.
Another thing, I don't always want to be my own player, stories are about interesting characters and making the protagonist a blank slate can work some stories but not character stories. It shouldn't always be done. Uncharted is probably one of the most far ahead on that front, by designing the sequences so that the player can be involved but will be doing the right thing, like when you're running away from the bad guy and all the cinema that happens in-game instead of in-cutscene.
Finally shout out to the bit in Uncharted 2 where if you try to take a punch at a guy you hate, he decks you and will eventually kill you. It explains the story (why isn't he trying to escape?) and it correctly predicts how the player will feel and stops the story and cutscene being disconnected like would have happened if the guy was just invincible to being punched.