The choices then being made not just in the dialogue and in the ALERT! scripts, but also in the fps-views. And this is what allowed you to follow that story as your own character, that you write your own justifications and ideas into. Instead of just playing back a premade one.

Agree that Kojima also achieves that immersion in MGS2. But it is with a different method. I really enjoyed MGS2 as well, though. But it bears to be mentioned that this game is enjoyable thanks to the writing skill, and the absurd characters and situations they're put in. Where that initial boundary to the extreme, that small zone you need to throw yourself into, is something the narrative requires you to do in order to accept the mechanics of the game and the universe itself as plausible. If only for a moment, so that when the suspension of disbelief breaks, you question what you've seen on your own, not what the game just played back at you..

If you've watched Evangelion, you recognize that type of story-telling very quickly. It's intended to make the viewer think about their own thoughts as they see the situation play out in front of them. It's profound and soft, and in the next breath extremely heavy-handed. And that is what is needed for you to connect with the situation the characters are in, to adopt yourself into the character's roles. Before being pulled out again, so you can see the fiction as something more than what the animation is playing back at you.

I'm just saying that Deus Ex was a very interesting and successful game, that designers now typically don't even try to copy. While MGS2 had an interesting story that in essence expects the player to invest themselves in it more than also modern Japanese story-telling typically requires. There is a reason why Miyazaki becomes less and less subtle in his scripts as time goes on (to the point where he essentially screams the plot at you during the scenes in Howl's Moving Castle). And there's a reason why things like Ghost in the Shell isn't created any more. Simple as that – this idea that you should expect total immersion from the viewer is not as popular when going for more casual and broader audiences. In any medium.

So both these two approaches to ambiguous narratives were very important in each of their own rights, I think. MGS2 for pulling the wall-to-wall carpet out underneath you at the end, after carefully decorating the entire living-room. And Deus Ex for allowing you to play the events that lead up to the very clearly telegraphed and in most ways singular conclusion, as if experiencing the actual events taught in a history-lesson, etc.

– To be fair to Deus Ex, it was released 1,5 years before Metal Gear Solid 2. That may not seem like much, but that means that there's a generational difference between the games (between the PS1 era and the PS2 era);
– "However, the best games must transcend the set of systems from which they are constructed." I couldn't agree more, but it's too bad that you don't mention anything about how the game systems in Deus Ex and MGS2 feed into its narrative. Instead, you focus purely on the story, and that the game designers either give you the choice of different endings, or the choice of different interpretations of the same ending. Which brings me to my last point:
– Though I vastly prefer a more ambiguous narrative to a clear-cut one (this seems to be a difference between western developers/audiences and Japanese developers/audiences: cast your mind back to the confusion that greeted the beautifully vague ending of Final Fantasy VII, for instance), this kind of "choice" isn't unique to the medium of videogames. So what is it about MGS2 that leads you to "embrace [it] as the true embodiment of everything [you] feel can be compelling about gaming" as opposed to art in general? (I mean, I can think of a thousand answers, but I'd like to hear yours. I mean, you're not afraid of spoiling a twelve-year-old game, are you?)