Something that's cool in Deus Ex, that I've never seen anyone remark, is that you have to work for your preferred ending. It's not enough to say "I want the Tracer Tong ending" and you push a button. If you aren't good enough at the game to complete your preferred ending's objectives in Area 51, you might have to settle for another one. This influences any philosophical or ethical conundrum you might have regarding the choice, and it's appropriate to the rest of the game. You want to keep Paul or Jock alive? Then play the game better.
By comparison, Human Revolution just gives you two buttons and tells you to press one of them. The quest "That Lucky Old Sun" from New Vegas falls into the same trap. You get to the top of HELIOS One and decide where to direct the power, the end. In essence, it's a separation of narrative from gameplay, which should be verboten in the RPG genre.