I think using the morally grey areas of life to explore your story is actually one of the most interesting ways to share your story out there. It's only used a lot because it offers so much to delve into, much more so than black and white stories. After all, how can your character be flawed when he's entirely in the right? How can a villain be compelling when he's completely in the wrong?
I feel one of my personal favorite ways this has been used is in the video game series Borderlands. Specifically, in Borderlands 2. The main cast of characters are the good guys, but as the game goes on you begin to question it. You're brutes, who wander a wasteland killing anyone who stands in your path and stealing their stuff. The planet is just as ruthless, full of monsters of all sorts.
The main villain, however, must be in the wrong, right? Well...not quite. Yes, he's definitely a psychopath, but his end goal is honestly...admirable. He wants to tame the planet of Pandora, make it into a paradise of his design. And how can you blame him, when everything and everyone wants on the planet wants you dead, including the heroes?
It's this kind of flawed ideology on both sides that make a story far more interesting. Black and white stories have their perks, the Superman storyline is going strong. But there are just so many good ways to tell a morally grey story.