In response to "A Videogame, in Three Acts" from The Escapist Forum: I've seen plenty of films that played fast and loose with the system. By and large, they were better for it. Then again, the overall introduction/question->resolution->climax/what then? provides one more good reason why Indigo Prophecy is jarring. It follows the formula perfectly (thus building expectations) until it goes bananas and then restarts somewhere after the beginning. It's like switching channels between two drastically different films on TV.
Interesting theories, but little more. As it's been said before, you can't apply the theory of movies and cinema to games, at least not directly. Your article mentions that you can't make the game more compelling by adding to the gameplay. To that, I say: Yes, you can. Play NetHack. The story fits in a small box of text. It's not compelling because of that, it's compelling because of the ridiculous depth of gameplay, far beyond most of the deepest games out there. It may be a special case, but even if you make the story more compelling while ignoring gameplay, it won't work - the gameplay has to help you out here. After all, it's what makes a game a game.
Another strike against it is that games are much longer than movies. A three-hour movie is long. A five-hour game is short. If you develop something in the first minutes of gameplay and hold it over the players' heads for the hours and hours of gameplay it loses its power over time. There are ways to reverse this, mostly renewing the conflict (also know as 'there goes the city again') but a better way is to solve issues while creating new ones.
In response to "String Theory: The Illusion of Videogame Interactivity" from The Escapist Forum: I remember hearing (somewhere... damned if I can find a source for it) that throughout HalfLife 2, it'll subtly tweak the amount of damage you receive to try and keep you alive for as long as is believable - you take less damage per hit when you're low on health, but not to the point where you're unable to die, or that you'd notice unless you were carefully taking notes on how much damage everything does.
Less player death means more time spent on the fun parts, more "just a little further, need to find health" tension, less repetition of parts you've already played through, I approve. If it were too blatant it'd feel like it was sucking all the challenge out of the game, but they seem to have it finely honed to the point where you always feel challenged, but don't feel that it's impossible.
I actually found this article really interesting, but not for what it said, so much. Rather, it was interesting to compare to ancient literary criticism (bear with me here).
The talk of games 'lying' to us by trying to convince us that there is more freedom on offer than they actually simulate is very, very similar to the ancient problem of literature 'lying' to us by trying to convince us of the reality of their fiction. These days, we talk about the ability of literature to help us 'suspend our disbelief' - we accept that while fiction is, well, fictional, it works best when it convinces us, albeit temporarily, of its 'truthfulness'. This doesn't bother us at all, but in early literary criticism it was a huge stumbling block to get over; there simply wasn't a culture of literature in place to allow critics to accept that while lying was bad, the 'lies' of fiction were an altogether different kettle of fish.
It would seem that games criticism is currently at that stage, where the 'lies' of games in their attempt to immerse gamers more fully are still seen as troublesome, and not simply accepted. I wonder how long it'll take us to get over the problem?
(It took the Greeks a few hundred years, by comparison)