A number of reasons. Firstly Japanese who committed war crimes were held responsible. At least some of the High ranking officials. The Japanese Imperial Family was not arrested and tried. The Truman administration and the MacArthur decided that having the emperor in place would legitimize the occupation government.

At the time as detailed in MacArthur's autobiography there was a great deal of concern about Stalin and the Soviet Union. The west desired a stable democratic government in the East. The eventual Marshall Plan in Europe was part of this movement to counter the growth of the Soviet Union.

The linked Wiki article details the Tokyo Trials. The Far east version of the Nuremberg trials.

http://en.wikipedia.org/wiki/International_Military_Tribunal_for_the_Far_East

Largely because it was understood that only removing the immediate threat would not 'solve the problem' as it were. The conceptualisation of Japan within Allied thinking was not simply of a regime to be removed, but of an entire political and social structure that needed to change (or be changed) in order that Japan be a peaceful and ideally democratic state in the future. It was not enough to simply defeat the enemy, but once that enemy was defeated a process of political and social reconstruction and transformation was necessary in order to secure future peace. In essence, making lasting peace was understood as requiring the remaking of an entire nation.

I would argue that this was in part due to the experience of Weimar Germany, in which while the military was limited and the state punished, the political and social structures weren't really changed and the 'problems' of militarism and anti-democratic forces not solved.

At the end of World War II the USA had two major things in mind. The first was not repeating the circumstances that led to World War II! That is, avoiding a Treaty of Versailles-like situation where the enemy would be humiliated and weakened. Why? Because they thought that produced instability in the short term, radicalism in the medium term, and war in the long term. The failure of the Treaty of Versailles to keep Europe safe had a strong impact on thinking about what to do after WWII.

The second thing was that there were Communists in Asia, encouraged by a strong Soviet Union. They didn't want Japan to go Communist — a real fear amongst both the US and the Japanese high command. The ideal situation for the US would be a peaceful relationship with Japan, using it as a bastion of US strength in the far east, and thus an additional ally between the USSR and the USA. So strengthening Japan, and making sure the right elements were in control, was seen as a vital US interest.

In both the case of Germany and Japan the US pursued a strategy by which eventually democratic governments would be given autonomy but kept very much within the US orbit, and both countries were hosts to substantial US military forces even after they gained their autonomy (including serving as forward nuclear weapons bases).

It was actually the same government - most of the bureaucracy - sans military - remained in tact to carry out SCAP orders. In fact, the survival of the prewar bureaucracy after the war was a big reason for SCAP's success - think of the chaos in post-"liberated" Iraq where the Baathist bureaucracy was dismantled.

Your question is a bit confusing. Surely you know that there were war crimes trials in Tokyo, Yokohama, and all over Asia. About 200,000 other elites were purged from government and business for suspected militarist sympathies.