Karune revealed the EMP ability is back in the latest build, under the Ghost’s arsenal.  The game mechanics are a bit different than in StarCraft not only for the EMP, but for the Shield regeneration which is twice faster.

Blizzard Quote:
EMP is currently on the Ghost and does 100 shield damage to all units and drains all energy in that area of effect. Having a Ghost presence in any TvP match up is crucial, especially if there are casters in the opponent’s army. In the original StarCraft, the EMP used to kill all shield hit points, but since in StarCraft II the ability has been added to the Ghost, which is more easily attainable unit than in the original StarCraft, we have reduced it’s potency a bit.

Plus a one-click ability that reduces an opposing army to half health near instantly isn’t something that we want to promote.

To combat EMP, Protoss players have huge new additions to their arsenal that can help them attack, defend, and buy time for tactical retreats (to allow shields to recharge since they recharge 2x as fast as the original StarCraft). These new additions would include but are not limited to: Force Field (Disruptor), Temporal Rift (previously known as Time Bomb) (High Templar), Colossus AoE lasers (with upgradable range), Phase Shift (Disruptor), Shield Regeneration (added to Obelisk [known previously as the Dark Pylon] replacing ‘cloak’).