While the quests and their storyline is good, the explanation of the big bad guy is terrible, I agree.
Also, every time I go in Blackwing Descent I think to myself: "Why am I here? When did Nefarian get ressurected? Wasn't I fighting the Twilight's Hammer? Did I really miss something?" (No really, maybe I did miss something )
It's funny how in WotLK Blizzard made sure so everyone knows Lich King is the big bad of the expansion, but in Cataclysm... it's kinda... meh how much Deathwing is involved.