I think a big factor in the relative ease of turning Germany and Japan to our side was killing millions of them first, and especially the men of fighting age. Nothing quite says "you should probably not rebel against our occupation" like slaughtering the people who would be fighting, and wrecking entire cities in the process.

Of course, such techniques would have been a tough sell in 2003. (And rightfully so.)

It's been postulated that purging the Ba'ath Party made rebuilding Iraq more difficult.

https://en.wikipedia.org/wiki/De-Ba'athification

The argument goes that a more measured policy could still have eliminated most of the bad actors while maintaining a higher level of governance and services.