For me, I think the Chosen One is such a cliche when it involves a "Good vs Evil" approach to it. I want some Grey area in the middle and some different elements to the story. Is the "Good" side wholly good or are they just the majority who wants to spite a minority? Does the Chosen one truly want to be the hero or are they forced to do so? There's also more development you can do when talking about the Chosen One or the people they care about. Does the main character even want this burden? Are their loved ones against their duty?
I think one way I've used the trope was through family tradition. For one of my comics, the main character is the "Chosen One", but only because of the duty that's passed down through her family. They took on the role, and it's her turn to carry it out. But even so, she's not willing to sacrifice her life that easily.
Cliches aren't bad per se. They're only bad when you take the same thing someone else did and just slap a new character in place. Sometimes, you gotta take them and twist it them a up like a pretzel.