That's all deliberate design choice. The original Deus Ex took place in (I believe) 2052, HR takes place 25 years earlier in 2027, and MD in 2029. The idea was to show how society tipped over into that dystopia in Deus Ex, and the only real way to do that is by starting with an apparent utopia, in HR, and having it culminate in the first major "crash" point. They needed to establish what the clean and idealized future was so that we could see how far things had fallen. I actually quite like that they took basically the entire plot of HR to establish that, rather than just hand-waving it away in the opening sequence.