The issue with Young Justice is that it was a great show with $#!+ merchandise, and since it's high production values and tone were expensive, it's cheaper to replace it with reusable animation and more...questionable writing. Cartoon Network's become less about good cartoons, per se, and more about cheap, dependable cartoons that require only basic skill to keep up and running.
It was obviously good enough to get a second season almost right off the bat, but somewhere a numbers cruncher decided it wasn't moving enough toys. Which I blame on the toy designers lacking imagination. BTAS merch had so much variety and advertising you'd end up with a small army of different Batmen. But Young Justice was kind of dull and ill-advertised.
Which is why the future for serious superhero stories probably belongs to live action shows. A manageable budget can attract the same audience as a high price cartoon, including the kids, but with a much greater appeal to that coveted 20-30 demographic. So Flash, the live action series, has a better chance than Flash: the Animated series. Mostly because the last ten years of movies and Arrow have illustrated how to approach the subject matter: make the conflicts engaging and the characters complex, and you've got a handy dandy mythology show set in the present day with a built in fanbase that will do half your advertising for you, and throw in a little fan service and get the "shallow" kids to watch and pay attention. Boom! Success!