Just started playing after a couple of years away from the series and I remember noting this but getting used to it in the last one too. I've just finished Dead Space and the movement in that is much more fluid and natural. I'm just wondering if the makers had some kind of blind spot when it comes to characters walking/running (running in particular), it seems unnatural and weird. I'm playing the female version, not sure if that makes any difference.
The main problem with shepards running is that his head attempts to follow wherever he is looking and no matter what his speed and his body position do not change. This makes for a very unnatural run/walk style when compared to a normal human being.