Then someone figured out how to get through the entire game with a zero body count. Deus Ex was such an emergent game with so many options, that a savvy player could actually do things that the developer thought was impossible, without resorting to bugs and glitches.
This. If somebody played Deus Ex without ever thinking outside the box, they missed out on the game's greatest strength. Judging by the comments in this thread, it seems like some people never thought outside the box and played through the game in the least creative way possible. Although DX3 appears to be offering combat, stealth and diplomacy options, I highly doubt there will be as much emergent gameplay as there was in DX.
Another great thing about DX was the attention to detail. Almost every little thing you did was acknowledged by the game. If you killed everyone on Liberty Island, characters would acknowledge that. If you killed no one on Liberty Island, characters would acknowledge that. If you left Gunther in his cell, characters would acknowledge that. If you hung out in the ladies restroom, characters would acknowledge that.