Honestly it just seems to me that people continued complaining on the Far Eastern themes and pandaren race rather than the storyline. Pandaria had an extremely dark expansion covered up with excellent subtly and that's one of the things Blizzard has always been good at, portraying a rather dark or traditionally epic-style storyline through sometimes very stylized characters. MoP probably had the deepest message of any expansion and actually did help portray the players as a lawful neutral force. At the end of the day, Horde and Alliance might only do what helps them and not necessarily what if lawful good. It also dealt with some darker themes recurring within the WC Universe (slavery, genocide, two peoples meeting).
Now things me to my point, with all the hate Mist got, do you maybe think it might've pressured Blizzard to go more "savage" more "awesome" which created out "beloved" expansion WoD. Not saying Blizz hasn't handled these themes well before, but did they bite off more than they could chew? Maybe they second guessed themselves with the storyline and rushed through it and especially underestimated themselves and raised their expectations.