Phasing is one of the most powerful tools in the designer toolkit. But like many powerful tools, it can cause great damage if used incorrectly. We definitely have overdone it in the past.
There is some phasing in Mists, but we try to take care not to separate friends, create ghosted mining nodes, and similarly disrupt your gameplay. What we were really referring to by the "dark secrets" is the way the story unfolds. The story in Cataclysm was something players knew from the outset -- Deathwing is back. The players were still heroes trying to undo some of the damage he caused, but they also still largely reacted to the things Deathwing and his minions had already done. In Mists we're attempting to take that one step further and have the world react to the players, and not just have the players react to the world. It gives the game a dynamic, "alive" feeling which is very much needed in a persistent-world game.
Some of the changes we're talking about aren't going to happen right away, but we'll build toward them in subsequent patches. While you can't truly keep story secrets in this business, we're trying not to spoil the surprises too early. In retrospect, we've taken a little bit of flak for this approach, because the misconception among some players is that the new continent has no conflict. There is plenty of conflict, but a lot of it begins when you arrive (rather than in Cataclysm, where great cracks in Azeroth appeared before your adventuring began).