There was a pronounced difference in the war crimes caused by each party, as I discuss here. The most famous case was that of the "Malay Tiger" Tomoyuki Yamashita, who was essentially charged with failing to restrain his troops when they committed war crimes. Specifically, Yamashita's defense argued that poor communication in the Japanese army made it virtually impossible for Yamashita to have any real control over the actions of his troops, and that he should not be held responsible for the actions of his men that he had no control over. However, he was still found guilty, under what became known as "command responsibility."

Command responsibility has been a very controversial legal issue, however, especially given that unlike Nuremberg, the Far East Trials were less of a neutral affair and more of one dominated by Douglas MacArthur, who acted on behalf of what he felt were US interests such as by exonerating the imperial family and granting clemency to the Japanese bacteriologists responsible for Unit 731, Japan's chemical and biological weapons research unit in China. It is also worth pointing out that among the war criminals executed was Masaharu Homma, the "Butcher of Bataan," who was also responsible for MacArthur's defeat in the Philippines. So make of this what you will.

I can only tackle part 2 of this question. The responsibility to disobey an unlawful order is not a new one. The oldest incident I am aware of is that of Peter von Hagenbach in 1474. I shall copy/paste from M. Cherif Bassioun, an scholar of international law.

Peter was a Dutch condottiere (a mercenary soldier) - the equivalent of a modern mercenary leader. Peter was hired by the Duke of Burgundy to raise an army to occupy the (German) city of Breisach and exact taxes from its population. The Duke had acquired the city in exchange for services rendered to the Holy Roman Empire. Uninterested in the fate of the distant German townspeople, the French Duke ordered Peter to collect massive exactions. When the townspeople rebelled, the Duke ordered Peter to sack, pillage, rape, and burn the city. Peter obeyed his superior's orders, as was expected at the time. The attack on Breisach was so horrendous that the news spread throughout the empire, bringing about an uncommon consensus that this situation was a 'crime against the laws of God and Man'.

The leaders of the twenty-six member states of the Holy Roman Empire, either in person or through representatives, acted as international judges to prosecute Peter, a Dutchman, for crimes committed in Germany on the order of a French head of state. For all practical purposes and in accordance with contemporary standards, this established the first international criminal tribunal.

"At the trial, Peter sought to exhibit the written orders of the Duke of Burgundy, but the judges refused to allow him to do so. Allowing this evidence would have conveyed the impression that subordinates in Peter's position should not execute the orders of their superiors when they are so manifestly 'against the laws of God and Man'.

He was sentenced to be drawn and quartered.

The principle has been sortof on and off since then. In 1921, a U-Boat commander was acquitted of torpedoing a hospital ship, given he had been ordered to do so.

On the US side of thing, the first time a US military officer was convicted after using the 'obeying orders' defense, was a US Navy Captain in 1799. During the War with France, Congress passed a law making it permissible to seize ships bound to any French Port. However, when President John Adams wrote the order to authorize the U.S. Navy to do so, he wrote that Navy ships were authorized to seize any vessel bound for a French port, or traveling from a French port. Pursuant to the President's instructions, a U.S. Navy captain seized a Danish Ship (the Flying Fish), which was en route from a French Port. The owners of the ship sued the Navy captain in U.S. maritime court for trespass. They won, and the United States Supreme Court upheld the decision. The U.S. Supreme Court held that Navy commanders "act at their own peril" when obeying presidential orders when such orders are illegal.

It is worth noting that there is still a standard of be met to override the orders from above defense. The US Manual for courts Martial has this to say on the matter in Rule 916: "It is a defense to any offense that the accused was acting pursuant to orders unless the accused knew the orders to be unlawful or a person of ordinary sense and understanding would have known the orders to be unlawful." Similarly, under Article 90 it states: "Inference of lawfulness: An order requiring the performance of a military duty or act may be inferred to be lawful and it is disobeyed at the peril of the subordinate. This inference does not apply to a patently illegal order, such as one that directs the commission of a crime."

As a result, the 'we were only obeying orders' defense is still quite a valid one in many circumstances. It's not enough that the order was illegal to secure a conviction. The person obeying it must also know it to be illegal, and be certain enough of this to act 'at his peril' in disobeying it.

I was speaking with one Scandinavian officer, I can't recall if Swedish or Norwegian, that they have what he described as a "Command imperative" call, which overrode any responsibility to an individual, the commander taking the responsibility himself. This reflects the realities of combat not being clearly defined. The example given was that if a woman and child are approaching a checkpoint, and an officer at another angle were able to see that they were wired for a bomb, and no time allowed for explanation. If he ordered the checkpoint to shoot the woman and child, understandably, the soldiers may hesitate. But if he said "Command imperative, shoot them", they would be absolved of the legal responsibility. The theory being that responsibility and accountability still exists, but is placed squarely on the person issuing the order as if he had been the one to pull the trigger himself. I don't know if this theory has been actually tested in law, but I do like it.