Out of all video games, Deus Ex predicted our current world the best. Its medley of conspiracy stories is partially ridiculous and it's easy to point out many details that don't hold up now but still felt almost prophetic in its prediction of the near future of the western world. It's losing staying power because of that. None of the System Shocks compare and they didn't try either.
No prophecies, just simply logical conclusions based on extrapolation of already documented events at the time. In 1907, 90% of Americans were self employed. In 2000, it was probably about 9%. Spitballing numbers. The American gov. already had a documented laundry list a mile long of absolutely sinister shit. Human history already had a laundry list two millenia and beyond long. There had been military leaks about a group named MJ12. And much more. What did Deus Ex otherwise predict? Gray death? Transgenics in the sewers? Self-aware AI? Bombing of the statue? West coast collapsing into the sea? All of that remains fictional. Otherwise the "writing" was pretty much on the wall already in 2000, they just had the perception to see it coming. George Carlin was already exposing back then. X-Files was a sensation. MiB movie. Conspiracy games that came before (Syphon Filter in 1998). Being conspiratorial-aware was kind of almost mainstream!
All this takes absolutely nothing away from the story though. It is extremely well written, conveyed, blended with gameplay perfectly, intelligent, and vital for spreading awareness of these matters. Most definitely my favorite video game story. And the most important video game story. Much of it isn't prophetic or esoteric except some very core themes, those being the most important of all (Population control, shadow govs, weakening individuals and strengthening themselves). This was still evident in 2000 though, so not prophetic, but most definitely esoteric yes. The common man would wave it off for sure. Lots of sheep.
Twin tower skybox coincidence is quite whack though! But it makes sense. They stood taller than the other buildings by quite some margin and texture dimensions in the unreal engine could only be to the power of two matching on both axes. I would imagine most games in 1999 with a NYC sky box would not have been able to feature it in one texture while having the rest of the buildings look proportional. Could be made its own texture and slapped in there though, just not worth the effort at all, that would be wasted time. An Interesting coincidence, nothing more.