As seen on Blizzplanet and scrolls of lore, Blackfathom Deeps has been completely revamped in the WoD alpha. All new bosses (except for Ghamoo-ra and Aku'mai, who both have new models and abilities), new trash mobs and a new story.
Here's a run through of it the updated instance: https://www.youtube.com/watch?v=ruf74YTJGjQ
And of the dungeon journal with new lore entries: https://www.youtube.com/watch?v=oEzL0KNL_hc