Well. The latest expansions have tried to balance the "Good vs Evil" towards "Grey vs Grey", so it's natural that each expansion drives the story in different directions. For instance, at one point the horde was actually the good guys (end of thralls era), so they decided to hand over the horde mantle to some nationalistic prick with a thirst for power, then he turned mega evil and the horde was suddenly the mega bad guys again..then they repented and got a super boring warchief..So now they killed him and handed us a really cool interesting warchief with loads of layers..but she is clearly on the evil side..so they had to make some of the alliance characters "crazy"..in comes Jaina Proudmoore
all in all i think they're doing a great job with the story. The only Stupid part is that Thrall vanished when he finally found peace and didn't return when the horde needed him the most as warchief.
And for the first time the alliance has a Gay leader aswell (not openly..yet..but clearly..)