Listening to Bill Van Buren talk about Half Life 2 I realised a key reason for its excellence - it shows you the story rather than telling you, just like a good author showing you rather than telling you scene details. it doesn't parade the story in a cut-scene but rather puts you right in the middle of it.
It's little surprise only Valve have really gone down this path properly as it clearly took a lot of work making the "cut-scenes" unbreakable by the player. The powerful scripting system did often allow the designers to create scenes without the assistance of animators or story boards - they just threw together a rough cut with existing animations and rough voice over files (apparently Marc Laidlaw created some great ones, so much so they were tempted to leave in his Father Grigory).
As you may be aware they spent a lot of time getting eyes right - how they focus and even how your eyelids dip when looking down. They also used real people as character references (I wish I had a photo of the slide, it was really interesting to see the comparisons), though they ended up stylising them somewhat as having them too realistic was "just creepy" as Bill put it. They're continuing to move forward in the area of facial animation and have even hired Bay Raitt who worked on Gollum's facial animation.
Their character animation system is particularly impressive too - at one point Eli Vance was running, looking to the side and typing (!), all blended in real time. To create a scripted scene you kind of layer things (an eyebrow movement here, a wave there and so on) and adjust line graphs to alter movement intensity. It's all extremely intuitive looking stuff so the designers can more easily get on with making the game.
One thing I didn't realise was that Half life 2 rewarded the inquisitive - players who looked around not only saw newspaper clippings and photos but in doing so triggered revealing comments from other characters.
Someone pointed out how much time was spent alone in Half Life 2. Bill replied that they were aware of this and were working on keeping NPCs with you for more of the time in Aftermath. This brings with it the problem of ever-present characters becoming irritating, but they're aware of that and working to address it so they're helpful rather than annoying.
One final interesting detail - they narrowed the field of view from 90° to 75° in Half Life 2, narrowing it even further to around 50° during the final cut-scene with Breen.
It's pretty evident just how much attention Valve pay to details and how eager they are to keep moving forward with new ideas. Aftermath can't come soon enough.