The firebombing of Tokyo[0] on 10 March 1945 is often considered even more destructive and lethal than either of the nuclear bombings of Hiroshima and Nagasaki, or at the very least in the same ballpark. However, popular discourse never treats it as a crime against humanity.
What is the qualitative difference between the killing 100,000 Japanese civilians in one morning using an atomic bomb and the killing 100,000 Japanese civilians in one night using explosive and incendiary devices?
Japan was the one who started the war. Japan was the aggressor. Defending yourself by winning a war against an aggressor is not a "wrong".
Many more people were saved by dropping the bombs than people died in it. And, while it is a tragedy that those people died, that fault lies with Japan, not the US.
The point of the concept of war crimes is that it applies to you regardless of whether you think you’re in the right. Even if the other side is committing them, it still applies. That’s why the definitions take pains to not make them a winning strategy or unilaterally avoiding them a losing one: why we talk about (deliberately) targeting civilians, not (incidentally) killing them; why putting munitions in a Red Cross-marked hospital annuls all protections for it; etc.
My thoughts about this after 50 years of thinking about it is that war results in a relentless normalization of deviance. It's a good reason not to start wars.
The notion of "crimes against humanity" is a very modern construct. The Japanese civilian society paid a price for its militaristic adventures. Armies don't operate in vacuum, they're an extension of their society.
The normal response to this line of reasoning is that they were / could have been doing the same to us. Two wrongs does not make a right does it?