It's an interesting thought. Plenty of games that are directed towards historical enthusiasts (as opposed to the masses who merely enjoy the glory of being on the winning side) do provide opportunities to play the Germans and Japanese. In fact, German armor is a favorite amongst those who play the Germans in strategy games, as is the Waffen SS and the Afrikakorps under Generalfeldmarschall Erwin Rommel. Many of you might be too young to remember Lucasarts' Secret Weapons of the Luftwaffe, (by Larry Holland, a precursor to the X-Wing series and to his Totally Games development company) which celebrated the robust air forces of the Third Reich. In fact, as Jackpot524 notes, plenty of simulators have considered Axis protagonism without concern for censorship or user disinterest.
As for changing history to let the baddies win, that's only a single option of many. Medal of Honor: Allied Assault didn't play to the end of the war, and neither necessarily would a story told from a low-ranking German officer. In fact, there are more realistic opportunities for FPS style heroism among the Axis armies, where a tight few protagonists stood off against an overwhelming enemy. (The sleeping giant that is America is, if anything, well populated.) And while most soldiers under overwhelming odds perished, some prevailed, and those stories are astounding regardless of the colors they wore.
The point also shifts depending on the intent behind a game. One doesn't ponder the ideology behind Serious Sam or Duke Nukem (despite the fact, for example, that the later has some obvious misogynistic elements) so the nationality of your run-&-gun hero shouldn't matter, either, so long as he (or she) ultimately saves the world in the end (usually from monsters darker than Nazis anyway). On the other hand, in a game that is meant to create an experience reflective of the Hell that is war (parts of the Call of Duty series comes to mind), any soldier that dutifully gives his life to his country is a hero, again, no matter the stripes.
Regarding the evils of Axis ideology, it would behoove us to remember: 1) The Final Solution progressed out of course from anti-semitism that prevailed world-wide. Them Nazis weren't unique in their opinion of the Jews, or in considering their eradication. 2) Neither the Third Reich, the Axis Powers or WWII formed in a vaccuum, but as the consequences of WWI and the harsh reperations demanded by the Treaty of Versailles. Both Germany and Japan were, to a significant degree compelled by circumstances to go to war. 3) Not everyone in the Wehrmacht was an Arian, Jew-hating Nazi eager to march into Poland. In fact, a growing majority of Germany's fighting forces were not, disagreed with the Nuremburg laws and the need for expansionism, but still felt duty to Germany, not the Third Reich, and certainly not for the glory of the Führer (albeit, he was rather charismatic). 4) Not a country on Earth is a stranger to attrocity, to crimes against humanity, or to war crimes. The German Holocaust does not serve as an example of a singular evil, but the magnitude to which they can manifest, if left to fester, unchecked. Certainly, the United States does not have the priviledge of moral higher ground.
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