One had piss poor management and the other one did not. There was a quote in one of the newspapers today from a retired JAL pilot. It was something like "If I had a gun I would find all of the CEOs from the last 20 years and shoot them in the head."
JAL originated as a state carrier and when they were privatized, neither JAL management or the government really understood what that meant. So JAL spent money like it was going out of style buying everything from golf courses to laundry companies, and the government "encouraged" them to fly to places that didn't make financial sense.
ANA on the other hand never was a state owned company and has tried to run a business that made financial sense.