I've skimmed this thread a bit and I have to agree with Gersen about the level design, it was actually fairly boring compared to the exploration of Deus Ex and SystemShock 2.
But what really let me down was the story. I don't think I felt any incentive throughout the game to carry on, there was no REALLY mysterious conspiracy and I didn't really feel like the investigator JC was in the original. You went from point A to B and beat people up or went around them through vents and sliding along boxes, reading a few emails and doing some incredibly cheesy bossfights.
Whatever happened to big plot twists? Becoming a world sought terrorist hunted by all? Suspense? Feeling of slight opposition from the enemies?
Reading the newspaper framing you for various things and disclosing your real name (if you entered something other than the default at the beginning of the game)?
Honestly, this felt like a stylish puzzler with shooting elements. Not a bad game relatively, but that's about it.