I think a lot of your disconnect comes from the changes to the Vale after 5.4. The Sha were actually built up fairly well over the expansion, I think, but never all at once. It was always in bits and pieces here and there. I'd recommend doing the Lorewalkers rep for some good storytelling by Tigger, but here's a quick overview that can hopefully fill in some gaps:
There was an Old God in Pandaria, and the Mantid worshiped it's seven heads (this is revealed when you hit exalted with the Mantid). Y'Shaarj was said to have "consumed hope and begat despair ... inhaled courage and breathed fear," and when the Titans slew it, with its dying breath it cursed Pandaria with the Sha. So the sha are, essentially, echoes of an Old God. The Mantid hate them because they are the barest shadow of a shadow of their master. The Sha have the ability to feed on negative emotions, making them stronger and people more susceptible to sha possession when bad stuff happens.
Garrosh believed there to be something under the Vale, and he was right. When he ordered digging in the Vale in the Dark Heart of Pandaria scenario, he found Y'shaarj's dead heart. He brought it to the pools of the Vale. The Vale had been previously established as a Titan experiment lab, similar to Un'Goro and Sholozar, but the waters of the Vale were special. These waters allow the Valley of the Four Winds to produce such large crops, and these waters have extreme healing properties. It's actually possible that the pools of the Vale may really be a much less powerful version of the Well of Eternity, given that they had a similar effect on the murlocs of the area (transforming them into Jinyu, much like Trolls -> Night Elves).
In the Patch 5.4 trailer, Garrosh dumps the heart into the Pools which doesn't resurrect Y'shaarj, but it does "revive" the heart somewhat. It also has the side effect of completely desecrating the entire area. Garrosh intended to use the heart as a weapon to crush any and all dissenters. This actually wasn't nearly as much of an **** pull as I'm making it sounds, since Garrosh had previously looked to use the Sha as a weapon, with multiple instances of this all expansion long.
Anyways, I think a lot of what you're seeing is because they did a really messy job of changing the Vale. I like that they implemented some permanent change for once with a major patch, but the Vale was integral to a lot of the storyline around Pandaria already, and they didn't do a great job changing it. For example, when you petition the White Tiger to let you into the Vale, that specific quest takes place after the 5.4 trailer, when the Vale has already been desecrated. But when you quest through Kun-Lai and deal with the corrupted Monastery, they trust you because the outsiders haven't **** everything (read, desecrated the Vale) yet.
I think this expansion's story was a big learning experience for them. We had a lot of story-focused patches and we had a lot of great, permanent, and meaningful changes to the world to reflect the passage of time. Pandaria wasn't nearly as static as all the previous expansions were. That said, they did a messy job of it in a lot of places. I think WoD is going to be a lot better.
Edited, Aug 31st 2014 7:41pm by IDrownFish