Well, there is a fundamental change in the probability model brought about by different scaling of characteristics and roll modifiers - also something I'm not really fond of, having had some very bad experiences with high level WFRP 2e play.
For that matter, new Fatigue is also awful - so many extra things to keep track of for so little gain.
Still, it's the wounds and AP that kills these rules for me, and not because of any particulars of how they were introduced, but because I find the very concepts inherently unworkable.