Let me know what you think, I could be blinded by nostalgia goggles of a sort, but part of the wonder was going back every time and finding another new tidbit or plot point that I missed before. There's an instance in the game where you "leave me behind, I'll hold them off!" You can leave, which is what I did the first time...but my second playthrough, I stayed, just to see what would happen. And the game actually accounted for this, letting you help fight with your partner and unlocking an entirely different plot thread.
I can't describe how walking out into the market in Hong Kong made me feel. The drab and claustrophobic helicopter base opening up into this sprawling market in an alien land... So, I'm exaggerating a bit, but still. They hit this tone just right, and the graphics were good enough that you could let your imagination fill in the blanks. You really felt like you were part of this complicated living, breathing world, and you were the only one who could save it. Fantastic.