I don't think the museum you want exists, especially considering the breadth and width of WWII. For Japan it started in 1937 and encompassed an area ranging from the US Aleutian Islands to Australia and from Hawaii to present day Myanmar.
I think a combination of museums would be required to satisfy the criteria.
I would recommend Hawaii as a possible location. In Hawaii you have:
This monument is a collection of museums, ships, and static displays. It has two museums discussing the war in the Pacific, including events prior to US involvement. It's heavy on the US and Japanese history, but you're looking for Japanese history. It does mention Japan's treatment of Asians, appears to be historically accurate (understanding there's compromise and bias in almost any historic work). This is also the gateway to the USS Arizona.
USS Arizona Memorial The start of WWII for the US and best represents a significant decision for Japan. You may have to get in line early to get your free tickets for the ferry to the Arizona Memorial, depending on the state of US sequestration cutbacks.
This is a building and a hanger on Ford Island about twenty minutes from the Valor in the Pacific Monument. The hanger was attacked by the Japanese and still bears some bullet holes. This covers Pacific aviation, not just World War II, but there is a dose of Japanese aviation including an diorama and pieces of a Japanese plane that crashed on a Hawaiian Island and the story behind the events.
The location of Japan's surrender for WWII, you can stand on the exact location of the surrender. Still bears the scars of a kamikaze attack. Otherwise it is a battleship museum.
This comes close to satisfying all three criteria.
Historically accurate, although it has a US bent, I'm confident that most military museums emphasize their countries militaries; consider the target audience.
Includes Japan's treatment of Asians But not in great detail, more tangentially. I don't think it talks about Japan's treatment of it's own citizens very much nor does it address things like the Rape of Nanjing.
In Asia or Australia It takes about as long to fly from Australia to Hawaii as it does to fly from Australia to Korea, depending on where in Australia you depart from. Hawaii isn't Asia, but I think Hawaii fulfills the intent.