Theoclymenus: Yes, HR was a bit "X-Files". As a Heidegger reader (I'm showing off now) I don't really believe in any of this stuff anyway, including the original Deus Ex, but I still think it was a good and plausible plot. I also think that the questions at the end were / are kind of relevant not only to the story's game, but also to the future of humanity. Love it or laothe it, science and technology are here to stay. I don't either love or loathe science and technology, but I think that it has to find a harmony with all the earlier discoveries of humankind : the great PHILOSOPHICAL truths, which STILL (and will ALWAYS) hold good. I think the Deus Ex : HR team did a great job. I went for Taggart btw, even though I thought he was a bit of a creep as an individual (but frankly all of them were !)
Emob78: When it comes to that X-files conspiracy stuff, I think Outlast did it right. They brought the CIA's mind control experiments like MK ULTRA into the plot in an interesting way, did so very subtly, and the tone of the game was helped by the esoteric subject matter. Deus Ex HR just kind of beats the player over the head with it all. Kind of reminds of the same problem the Mass Effect games had. Too many different meandering paths and subplots. Sometimes less is more. Don't insult the player's intelligence, but don't also assume that he's an electrical engineer who graduated from MIT with a 4.0 in super villain studies.
I haven't played Outlast but it's on my wishlist. As a former philosophy student and lifelong (well, since I was about 13) lover of computer games, my idea of the perfect fusion of ideas would be Planescape : Torment + Deus Ex. Science plus spirituality is, I guess, the future which humanity (in reality and not just in computer games) is heading towards anyway. The technical brilliance of the scientific mind plus the bottomless depth of spiritual truth, which, in a sense, will always outstrip any scientific insight.
Navagon: I think that the ending of Deus EX HR warrants an exception, given that it was crap. Same old tacked on at the last minute 'push a button to get the outro of your choice' bollocks we got with Mass Effect 3. But at least these endings were more than just colour changes.
But generally though I don't really have a problem following most game storylines.
I think DXHR did raise good questions regarding science and technology. I'm not saying it was necessarily a good way to end a computer game, but it was a pretty good summation of the choices open to scientific-technologic mankind. It just didn't go into actual philosophy very deeply.