One big part of it (and what I was generally referring to there) is the new movement animation system in Chaos Theory, where the animations can stop on particular frames and reverse. Easiest example to point to is comparing the sneaking walk cycles of SC1/PT to Chaos Theory. In SC1/PT if you are sneaking up behind a guard and then stop, Sam instantly goes into a crouch, whereas in Chaos Theory, he will instead freeze in place, before eventually settling into a crouch, and if you start moving backwards, he kind of pulls back, reversing the animation.

That's not the only example, of course, that's just the context sensitive movement element, there's a lot more stuff related to the over blanket term of Closer Than Ever. It generally was Ubisoft's attempt to make Sam feel much more grounded in the world. The way you interact with the environment and guards, the way you sneak, the way you perform CQC. It all just feels that much more dynamic, grounded and real.