I still think that "System Shock 2" was better than the original "Deus Ex". Don't get me wrong: I loved the original (even if I do admit I like HR more overall, except for the music), but "System Shock 2" just clicked more with me: it had a much more involved character progression, story was much, much better and I up to this day consider Shodan to be the best villain of all time.
But as Marik Bentusi said: the philosophical conundrums and the A.I. events aside, the story in "Deus Ex" is very cheesy and I understood that better after I replayed it only recently on my PS2 (I was 15 when I played it the first time, was hardly a critically thinking fellow I am now). What "Deus Ex" got that "System Shock 2" didn't have was the freedom from which one could approach a problem. "System Shock 2" suffered from a more "head-on" approach, as most games suffer from (except for "Hitman: Blood Money", the only other game like that in my memory). Still, even "System Shock 2" had that to some degree, it was just more prominent in "Deus Ex".
[WARNING: might be considered a spoiler]
I was delighted when I hacked a terminal at the Spec-Ops base in HR, killing about ten soldiers through a hacked turret. That's what "Deus Ex" is and should be: freedom of choice.
[WARNING: end of a potential spoiler]