One of the (many) features which made Deus Ex stand out from the first person crowd was its use of nanotech augmentations, which the player had to choose between when "upgrading" their body. According to lead designer Harvey Smith, talking in an interview with RPGVault, developing and balancing the augmentation system was one of the big challenges in designing the game.
"We spent a long time going back and forth figuring out just how to do this. Should the player be able to add new ones at any time, or should a medical NPC be required to add them? Should the player be able to add an aug, subtract one, then add a new one to the same slot, or should adding an aug be permanent? Should they consume some resource like energy? How does the player 'get' one of these new powers?"
"This stuff alone took months, off and on, to work out - while we were simultaneously working out much more. Then came a slew of questions like which powers we wanted to let the player have. What does each tier of the power represent? How much energy does each aug drain? And, of course, until the aug system was worked out and the augs were actually in the game and tuned, we were not even sure if they would be fun and complimentary."
Of course, now that they have it all worked out and have seen it working in-game, developing augmentations for the recently announced sequel should be much simpler. "For Deus Ex 2 we already know the answers to those questions. Plus we know what made the augs fun and what made them less fun. So we can improve upon what was there much more quickly than we were able to set up the augs in the first game."