JL's main problem is that all of their flagship routes are 1000 miles too long. None of these routes can be flown out, turned, back, and turned again inside 24hrs. As the route has to go at the same time each day, the planes are always going to be out of whack and "underused".
Also it allows them to time the flights for when people want them. Particularly the JFK flights, there is potentially a case for shortening the turn and going to a night flight, but clearly they've decided a 1am depart 4:30/5am arrival is too brutal. But they are hardly the only airline who has low utilisation on their most important routes.

Qantas for example has only 12 A380s. A scare resource, but they leave them parked up for 14hrs a day down route in London, 7hrs in Dallas, and 2 of them park up for 15hrs at LAX. In Singapore, the a380 from Melbourne is turned in a comparatively rapid 2hrs45 whilst the one from Sydney takes 4. All of these are done to maximise how many of their routes leave after 7pm local and land earlyish the follow morning. High utilisation is good on paper, but not if it means flying the plane empty..