Man, 50 years of fighting really hit both Jack and Aku hard.

Well, to put it short. Failure is the greastest torture.

He saw himself as this big almighty being, able to conquer words. But for 50 years he was never able to beat this one man. He was able to take planets but one man was always above him. And no matter how he tried, no matter what he planned and no matter how many men he send against Jack. Aku always lost.
And with 50 years of defeats, he destroyed all of Jack's ways back to the past and decited to let time kill Jack, but even that didn't work.

So now Aku has to live with the fact that there will always be a man that can beat him out there in the world. And he now has to live with the fact that he isn't the almighty god he once was.