I'm sorry but I don't remember a sequence in either Planescape and much less in Deus Ex where the storyline focuses on examiniing and discussing various philosophical issues for almost an hour straight, ala MGS2.
Then your mind must be seriously fucked up.
First, A story isn't better just because of how many themes you pull out of your ass. In MGS2 various themes were touched (not as many as Deus Ex), but how they were shown to the gamer was nothing more than a clusterfuck, and a shallow presentation. Almost every time the themes were brought up was in such a superficial way like the characters talking directly about them, rather than just let them be noticed indirectly like through simbology across the game.
Planescape: Torment has the best game writing of all time, and the best plot. It reached into the deep infinite hole when showing their themes: Immortality, auto-analysis, alternation and confrontation of self, and punishment. Those were the main ones, but there were a few small ones such as confidence and mistrust, consensus reality, etc...
As for Deus Ex, hell, it touches more themes than the entire MGS series (as I said before). Those themes hide in the seemingly generic plot, and spur out mostly on an indirect fashion, and it when it was directly it was well written, concise and bending perfectly in the story.
I seriously hated MGS2's
Character1:"did you know religion blah blah?"
Character2:"Oh my god religion blah blah?!"
Character1:"yeah, 15% of blah religion blah bleh!"
One Thing I know is Kojima CAN'T make a great complex story.