Is an ekranoplan less efficient than a regular plane? This are my conclusions upon researching the matter:

Ground effect is the cushion of air that can not escape down because of the ground. The hovercraft creates that cushion using a skirt which prevents as mush as possible a lateral escape of the air from underneath the ship. In effect a pressure differential between underneath and over the ship is created, enough to counter the ship weight. The value of this overpressure is within millibars.

Now returning to ekranoplan. While in the water, the ship has to fight the water drag. If the wings provided just enough lift to defeat the water drag, and the air cushion former under is rendered slow enough at escaping, then the ship becomes airborne. Will ride on a dynamically forming air cushion, better known as ground effect. However, the air drag becomes now the main opposing force. Increasing the angle of attack will increase the air drag and thicken the air cushion to the point where the ground effect is lost and the aircraft will loose altitude down to ground effect. Since the power output is limited, the machine is restrained at flying in ground effect only.

Now in terms of efficiency, the answer is no. The ekranoplan uses more thrust to fly in ground effect because it has to overcome air drag which is significantly stronger due to high angle of attack required to maintain the ground effect. The main reason the airplanes are efficient is due to low drag cruising. The wing develops enough lift to maintain the aircraft in the air while the angle of attack makes the wing a blade cutting through the air. Since the ekranoplan rides at way lower speeds than a regular airliner, it is required a high angle of attack which in turn determines a high drag.
There are a couple of inaccurate trains of thought in the question.


  The ekranoplan uses more thrust to fly in ground effect because it has to overcome air drag which is significantly stronger due to high angle of attack required to maintain the ground effect.


All aeroplanes need to overcome air drag, which grows quadratically with airspeed. Ground effect creates more lift at a given speed, therefore requires less thrust at that speed. Or: ground effect creates more lift at a given wing area, requiring less thrust than the larger wing required for the conventional aeroplane.


  ...thicken the air cushion to the point where the ground effect is lost and the aircraft will loose altitude down to ground effect.


Thickening an air cushion cannot result in losing ground effect. The ekranoplane cannot fly out of ground effect - increasing Angle of Attack does not make much sense and altitude will auto stabilise to within ground effect, indeed at higher thrust level at higher AoA for a given speed. I believe this is what OP means, but it does not equate to ekranoplanes being less efficient than conventional aeroplanes. Ground effect creates extra lift without a drag penalty.

Whether ekranoplanes are more or less fuel efficient than standard aeroplanes is not due to the ground effect, but to the interference with the water surface, sea state, having to lift the engine out of the spray etc. Depending on the speed, they may be less efficient than ships, but the payload arrives a lot quicker.