for me it was mostly the console-support leading to the simplified inventory and skills, and the teeny tiny levels. the best thing in Deus Ex was the flexibility of play that allowed you to, say, fire rockets onto the top of a tower you were later going to ascend from the inside, or snipe people from half a screen away.
in the dozen or so times I played it, I think I only actually had the scripted sword encounter with that one person at the bottom of the big storage area once - and that was just to see what it was like. every other time, head-shot from the top of the ladder
nothing quite so fun or memorable in the sequel, which watered down everything.
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