As a mainly Alliance player my biggest damning pet peeve of them quest wise was finding out how much we missed out on/was cut to finish out the horde side.
Severe let down on their part.

what?

If you start a Worgen the entire starting zone for them is a big ramp up in the fight between them and the Foresaken. The ending doesn't have any kind of resolution though. You just survive long enough to get rescued by a boat.

You have to roll Horde and quest through Silverpine alongside Sylvanus to see where the Worgen/Foresaken story actually ends. To my knowledge, the Alliance has absolutely no explanation as to why Godfrey & Company are undead and in charge of Shadowfang Keep now. If you roll an undead and quest through Silverpine though, you get the entire story picked up from the end of the worgen starting zone and finishing up with... well lets just say the foresaken characters have a VERY good reason to storm Shadowfang Keep and mow down anything that moves in it.

@gewalt on cut content: Minimal draenei input, Alliance leaders not appearing in quests, Worgen essentially being dropped past LV12, completely scrapped Alliance Highlands introduction event while the Horde equivalent remained, an Arathi Highlands revamp for the Horde yet none for the Alliance and no explanation delivered for Deathwing appearing in Stormwind (which was likely Onyxia's head but was still never mentioned) amongst other complaints.

Which is not even mentioning all of the OTHER areas in which Alliance fans can criticize Blizzard.

How about the abrupt ending of the worgen storyline, which continues only for Horde players.

Whoops, guess I should have reloaded the story at some point in the last hour.

But really, this storyline was just howlingly bad in its execution.