I played it through two years ago, and the only thing that seemed really antiquated was the UI. Everything else was still pure gold, and it (along with System Shock 2 and Thief 2) is definitely still worth playing if you haven't played it yet. The plot, especially, is still somewhat remarkable for its degree of being "way out there" while still being compelling and making sense. And very few games to this date have done the whole " your decisions have repercussions " as well as Deus Ex did.
Another note-at least give Invisible War a try when you are done with Deus Ex. It's not a bad game and also still holds up pretty well, though it is clearly not the legendary game its progenitor was.