The one peeve I have with it is the overuse of crouch-jumping. It's used a lot more now to jump onto things that didn't originally need it. Almost like they designed things a tad too high and barely reachable when it looks like it could be reached with a normal jump. Jumping onto boxes or barrels is an example. It feels awkward.
I'm almost inclined to feel that the physics actually act as a detriment so far. There's nothing inherently designed about the game taking advantage of the physics, unlike say HL2, which I thought would be one of the things they'd be taking advantage of in the redesign of the levels, but when you do come across it, it's frustrating as you can't manipulate objects like in HL2, ie boxes and barrels.