There has been people discussing the new Deus Ex3 game and frankly I can't see how the plot will deal with the multiple endings of the second.
See in the first game you could either, join the Illuminati, merge with the big supercomputer or destroy the internet.
The second game added onto the first by saying that JC Denton eventually merged with the supercomputer and caused a global collapse of all technology. It's a bit flimsy, but there is a possible fit to all the endings.
Now at the end of the second game you can either join with JC and make the whole world think with one mind. Join with the Illuminati and continue as if nothing happened. Join the Templars and renounce all technology. Or kill everyone and allow the Omar to takeover the world, but ensure humanities survival into infinity by changing the race into cyborgs.
How the hell the plot of the third game is supposed to allow for everyone to change into cyborgs and discover new technologies, while denouncing all technologies and returning to a medieval like lifestyle is impossible. However I am sure the third game with whatever they do with the plot will be far better than the second because frankly the second game was crap, although I did enjoy it.