If you haven't already, make sure you have opened up the pressure relief valve on the water heater.
The pressure relief valve being opened will vent the water heater and help the water heater drain faster.
Other than that it might just take awhile to fully drain out depending on the size of the water heater.
Also once the water heater drains down you should turn the cold water side on and let the cold water coming in flush the sediment out more for around 30 minutes.