Not only did we stay for decades, we knew and expected we'd be staying for decades. We let them have a civilian leadership structure, but there was no doubt who was calling the shots - either with that leadership or their civilians.
Contrast that with how we handled Afghanistan and Iraq. We got a civilian leadership in there, but didn't drip out increasing decision making powers to it, we simply gave it far too much too quickly in the auspices of 'look we're not really taking you over, you guys are largely in control of yourselves'. Mixed in with the current US attitude of, If it can't be done McDonald's fast at Wal-mart prices, Commence Full Whine and Second Guess mode. Throw in some scum Politicians and Media doing what they can to subvert success and you've got failure written on the wall.
The lesson of Iraq and Afghanistan isn't that we can't conquer and institutionalize nations to our approximate way of thinking - we can, Germany and Japan proved that. It's that we can't do it on the quick, cheap, or politically correct. We're going to be non-politically correct when we need to be, it won't be cheap, and it will take 2-4 decades of concerted effort. It's why we keep failing at it over and over...