The surrender of Germany was unconditional. The surrender of the Japanese wasn't. The Japanese demanded conditions and got them. One was retention of the Emperor, another was that the Emperor would not be held for warcrimes.
Another condition that is always overlooked: while the Japanese MILITARY surrendered to the Allies, the Japanese GOVERNMENT did not. That is an important distinction to make.
In the end, MacArthur used the Emperor to good advantage.
Hirohito was a weak man that could be manipulated and used as a tool and, in MacArthur's hands, he became a useful tool for the good of Japan's future as a modern democratic nation.