Empolean isnt a counter. Kingdra uses Rain Dance upon the switch, boosting water attacks and blah blah blah. Kingdra outspeeds, and uses Hydro Pump.
Under the rain and with the EVS that Oceaniclanturn gave it, it does 34.7% - 40.9% (calculating Lefties in), a clean 3HKO to Empolean
Ice Beam with the EVS that Empolean has does 36.3% - 43.2% to Kingdra, a clean 3HKO however Kingdra outspeeds, therefore winning.
Grass Knot with the EVS that Empolean has does 38.7% - 45.5%, a clean 3HKO, however Kingdra outspeeds, therefore winning.
Surf is quadraple resisted, and does a meager 20.2% - 24% to Kingdra, barely scraping past the 5HKO
I shall continue...
Kingdra@Choice Scarf
Trait: Swift Swim
EVS: 252 SpA; 252 Spd; 4 HP
Nature: Modest
-Hydro Pump
-Draco Meteor
-Dragon Pulse
-HP [Grass]