It's not like they're turning it into a space opera about alien impregnation. It still follows the same ideas and themes that drove the first game. I know I wouldn't enjoy a Deus Ex game set 17 years in the future where they still drive 90s-era cars, where blogs never existed, soldiers wearing Gulf War-era outfits or even no cell-phones.
What I do appreciate, is that EM is trying to build the future with the same zeal that drove the original Deus Ex. While not everything is going to be as it is predicted in Deus Ex, the game's events do follow a well-researched canon. Not all of it was perfect, and the flaws are becoming apparent 10 years after the game's release.
EM is trying to update that with the ideas and visions for the future that have come to fore in the past decade, after the release of Deus Ex. I couldn't care less if they outright broke the canon, I already regard the two games as being different universes altogether (it's a bit of a given, after Invisible War).