I know my opinion in meaningless on this matter, but I don't see the controversy with the Japanese paying respect to those that fought on behalf of their country. Were such soldiers on the side of angels? Or on the side of devils? I cannot say, none of us can. I can say, however, that no matter what side people fought on, that they were people. Some were cruel. Some committed horrendous acts. Some regretted their actions, and some died before they were able to.
I say this: Let Japan honor their fallen soldiers, let the politicians honor them. Let them honor what they did so that nothing similar to it may occur again. The world must never have a World War III. The bell cannot be rung thrice, it will irrevocably ruin us in the end.
Well, I basically share your opinion, Thor, however, various groups with different political agendas have turned the issue into a boiling pot: the uyoku dantai, Japan's right-wing groups, as well as groups from neighbouring countries who play the Class-A war criminal card to have a cheap shot at their former enemy. Anyhow, I really recommend to visit Yasukuni's Museum of History, it's unique in some of its perspectives...