The way I see the one sidedness of games depicting WWII (for example, no German campaign in any COD series, Coh2, etc) is just propaganda that still to this day says Allies = good, Germans = bad.
While games that depict WWII deliberately try to distance the German military from Nazism (perhaps in part due to Nazi symbolism laws in some countries like Germany and Poland, for example), it's hard to do that. Steel Division has two SS divisions, and coh even has "Stormtroopers" which isn't exclusively a Nazi-German thing but has extremely close ties w/ Nazi Germany.
It's not propaganda that the Germans are depicted negatively.
Germany invaded Europe. Like, almost all of Europe. It's hard to sympathize with an occupying and invading force.
The Waffen SS did commit war crimes despite it being the military arm of the SS. The whole "Waffen SS didn't commit war crimes" was post war apologist literature propagated by former SS officers who didn't want to be tried for war crimes after the war (there were a series of Nazi-related trials before and after the Nuremberg trials).
Also, certain Wehrmacht units helped the Einsatzgruppen and police forces commit atrocities in the USSR, either directly or indirectly by providing munitions and logistical support. A lot of those units ended up being encircled in Stalingrad in '43 so they couldn't be tried.
Many high ranking Wehrmacht officers knew of the Wehrmacht's assistance of the SS in committing atrocities in the USSR.
And this isn't mentioning the reprisal actions taken against civilians for wounded/killed occupying German soldiers in Western Europe.
Basically, the Wehrmacht contributed, both directly and indirectly, to the killing of innocent civilians and the Holocaust during Nazi Germany's occupation of Europe.
It's not propaganda that Nazi Germany was bad.
Sorry, Mistah S.