By definition brake thermal efficiency is brake power produced divided by fuel power consumed. Firstly, the thermal efficiency of either a two or four stroke engine is a function of compression ratio. The nature of this relationship is complex, but efficiency is higher for a higher compression ratio. Putting it simply, a higher compression ratio causes higher pressures and temperatures in the cylinder and allows more mechanical work to be extracted for the cycle. The second reason two strokes have lower efficiency is due to gas dynamics.
Gas flows are complex in a two stroke in comparison to a four stroke.
Two strokes like to perform in certain rev ranges when scavanging is occuring in a favourable manner. Here expansion waves are cleverly used to draw mixture through the crankcase and transfer ports and provide improved cylinder filling. Unfortunately, this only occurs in certain rev ranges depending on the pipe geometry and port timing and shape. Out of this favourable rev range the engine can suffer from inlet charge contamination by exhaust gases, or fresh charge being drawn unburned into the exhaust. The direct injection system will reduce or perhaps even eliminate the environmental side of the problem, but the gas flow problem will still exist.