Ya know, this makes perfect sense. We all know that at some point, we're going to get to play as Desmond in the real world (at least, I've been crossing my fingers). Seeing as though Desmond is American, it makes sense for him to be played in his natural environment. Setting the ancestor in the same location can make for some INSANE gameplay and plot points. At this point they could build him a portable device that would let him look back and forth to the past. You could switch between time periods, sorta like in the movie Deja Vu. I just think that would be insanely cool.
I've really been interested in how the Assassins Creed franchise would handle modern day parkour. Mirror's Edge looked great, but I didn't get it because I heard the controls and gameplay were terrible. Climbing modern skyscrapers would be fucking amazing.