The story is great even after WoW, if only you look at it from a considerate perspective. The fact that Malygos was killed by random adventurers bother me, but Blizzard has always found a way to make such things work. Onyxia being dead is in lore not random adventurers, but rather Varian x2, Jaina, Broll, Valeera and some others.
My point: There are some sad cases in WoW, but Chris Metzen and the crowd almost always make it work. I'm glad they made Dar'Khan as powerful as they did, and not some second rate magician that wanted to make a buck.