I get that, but my discomfort with the idea is similar to my one with CSA-victory TL's: while you may get a good story out of it, too often it verges into Confederate/Nazi apologia (not so say I'm accusing you of that, just that it's a recurring issue).
Fair point.
To that end, what are some war crimes a "saner Axis" might still commit?
Here're some ideas:
*Overzealous junior officers who avoid getting purged in Japan still brutalize their men and inculcate them with pseudo-bushido nonsense, so we still get war crimes in China and abuses of prisoners in the Pacific, albeit perhaps not as widespread and with more punishment for the offenders.
*Anti-Semitic violence tolerated in occupied Soviet territory on the grounds that these are the common folk of the land avenging themselves on their Communist tormentors.
*Expulsions of Poles from German-heavy areas of interwar Poland to ensure demographic German dominance.
*Bombing civilians with the goal of getting them to pressure their governments into making peace on German terms a la Rotterdam in OTL. Given how anti-democratic many of the not-Nazis still were, this kind of terroristic attitude seems plausible.