Germany (Nazis) - Brutal war machine disregarding human life, industrializing genocide and doing everything to achieve their goals, like indiscriminately wiping out population in lands of nations they deemed "inferior" just so that they could claim it for themselves. They had concentration camps using people for forced labor, and also death camps where they straight up killed civilians of "inferior races" (including children). Holocaust, mass-murders, even using child soldiers and elderly when they got desperate on frontlines in 1945. They experimented on living humans in brutal manner.
Soviet Union (Communists) - Ruthless industrial powerhouse disregarding human life, committing ethnic cleansing and genocide but not because of racial supremacist doctrine (different from Germany), doing everything to achieve their goals, including purging its own citizens that dared go against the regime. They invaded Poland from East alongside Nazis in 1939, and committed mass-murders and massacres there. Holodomor in Ukraine, mass-rapes in Germany, ethnically cleansing entire Prussia and also existence of Gulags. They also experimented on living humans.
Japan (Imperialists) - Ruthless Empire doing Imperial things, but in 20th century, this time with Hojo pulling the strings. They committed mass-murder to terrorize civilians, indiscriminately bombed cities, enslaved people, with end goal of dominating other nations and growing their territory. Probably the most zealous major power during WW2, there are cases of soldiers killing their own families just to be able to become Kamikaze pilot and one of them continuing to "fight" the war for 29 years after 1945. They performed brutal human experimentations too.
Italy (Fascists) - A dictatorship seeking to dominate other nations and grow its territory. They often killed POWs and mistreated civilians, had concentration camps, committed mass-murders, indiscriminately bombed cities. They also stole food and other things from civilian population which resulted in starvation of hundreds of thousands, f.e. 300.000 in Greece alone. Not "as bad" as above three but only because Italy was very incompetent at everything they did, even failing to properly invade Balkans without German help, and embarrassing themselves in Ethiopia earlier.
Now about the two major Western Allied powers:
United Kingdom - They attacked a neutral country (Iran) alongside Soviets from North, attacked non-combatant ships, shot shipwreck survivors, tortured POWs, terror-bombed cities indiscriminately and looted a lot of places. Just like every other power, their troops committed rapes too.
United States - Indiscriminately bombing cities, terror-bombing, carpet bombing, nuclear bombing. They often shot surrendering soldiers, executed POWs, even massacred civilians on several occasions. Like the Brits, they didn't behave well either during naval combat. They bombed a neutral country "accidentally" a few times (Switzerland). Rape was common practice there too, as every country did it.
You can see that everyone did some bad shit in WW2, but you have to be blind to think US and UK were on the level as Axis powers and Communists in USSR. Everything bad UK and US did was also done by Axis powers and Soviets, besides nuking. On one hand, you have otherwise normal countries whose armies committed war crimes, while on the other hand you have a Nazis, Fascists, Medieval Empire in 20th with official murderous policies, not just their armies doing bad shit. As for the Soviets, while their leadership was definitely evil, most people living there were fighting for survival against Nazis, and many of them were forced into living in USSR with Red Army invading their countries two decades prior to WW2. So if you want to rank who was more "evil", on top would be Axis powers, followed by USSR, and then Western Allies.
Still though, there were good people on every side. A lot of people were victims of circumstance. Most people living today thinking they'd be heroes if they lived during WW2 are gravely mistaken. It doesn't take much to turn a normal human into a murderer or a criminal. Most of us would've been Nazis if we lived in WW2 era Germany. You have to read history from perspective of the villains, heroic people are and always were very rare.
Everything aside, this manga is still good, art is nice and it's a fun read. I don't care about author's intentions, as long as manga is fun I will keep reading and if you don't like it, nobody is forcing you to read it.