Here is an excellent blog post that covers much of the problems -
http://childrenofwrath.blogspot.co.u...red-story.html
While I feel guilty every time I bring it up because the topic was beaten to death months ago there were problems on a faction related level and on a villain level.
The part not raised in the post that I feel was a problem concerns Deathwing. For starters Deathwing had gone from the evil Dragon that spent his time plotting evil deeds and trying to create the most powerful Dragonflight on Azeroth while twiddling his moustache and manipulating the Human Kingdoms while doing this.
Cataclysm Deathwing was more or less a different Deathwing. He was almost insane, completely consumed by his anger and hatred and was executing his plan more through brute force than cunning tricks.