In Japan, when the government surrendered, the fighting was essentially over. There were no foreign powers with any great interest in fighting us in Japan (the way that various terrorist organizations are in Iraq), and the Japanese weren’t really prone to fighting us for various reasons. Their culture would’ve seen it as a great disgrace to go against the emperor and not accept the surrender, plus we’d pretty much destroyed their will to fight, I think, after Hiroshima and Nagasaki.

In Iraq, the government didn’t so much “surrender” as “get completely obliterated”, there are foreign powers fighting us on Iraqi soil, and we have been extremely careful about avoiding civilian deaths. (Which may not be an entirely good thing, since what we’re effectively doing is making war less horrible, which makes it more likely that our enemies would want to risk war — I’m reminded of the Star Trek episode, “A Taste of Armageddon”.)