Larry, I read "Flags" and tried to read "Flyboys" but was struck - as you were - by the moral equivocating. Turns out that the author spent many years in Japan and has a Japanese wife. I thought he was a bit of an apologist for Japanese atrocities. That's where "The Great Raid" really shone.
When I think of truly great war movies, the first one that comes to mind is "Zulu," and the second is "Patton." One thing that both of those have in common is there is no moral equivocating over what was right or wrong.
I'm sorry that Japanese cities had to be torched before their ghoulish, insane leaders would surrender, but them's the breaks. Better they fall into our hands than we into theirs.