Everything after Jade Forest is just kind of us cleaning up the horrible mess we caused at the end of that zone.
So the Empress wasn't a problem until the horde/alliance came?
Well, not as bad at least; The unleashing of the Sha weakened Pandaria (figuratively) and have the Mantid a new avenue to attack.
At least that's what I gathered from the quests. You know, that provide lore, which answer the exact questions you have?
Psh, that would involve reading them and then not only would it take me longer to reach 90 (meaning I'd have less time to complain about no content) but then I couldn't keep saying 'lollore' like I actually know what's going on! (which I obviously don't because I don't read the quests and then complain about how there is no lore)