Yes, cliches are cliches for a reason. But they also stifle originality. If I ever see a movie/TV listing stating "X is not like other teenagers. He has a power to XYZ", then I know that towards the end of the first/start of the second act, we will be introduced to a shadowy mysterious organisation of unimaginable power and wealth who are after the character, either the cause or the enemy of the power. And, every single time, it turns out to be a correct assumption (with the one exception I stated earlier).
This is boring. There is no need for a shadowy organisation. A story about people with superpowers does not need a shadowy organisation. It's just writing in cliched shorthand and lazy plotting, as far as I'm concerned...."Everyone knows X-Men, let's just take something off the peg from there..."
But what if you turn this cliche upside down? What if after a long fighting
against the organization, the hero eventually understands, that he should
support this shadowy organization, not fight it, because he is wrong, and they are right? And what if this organization is not as strong as it seems?
My story is about a very rebellious person, who eventually turns to work along with the system. And the antagonist, who is not a rebellious type, turns a rebel. The point is, that at the beginning, protagonist and antagonist
work together, trying to overthrow the organization. But later, the protagonist betrays the antagonist (for a good reason), and helps the organization to stop him.
There is a dilemma. The antagonists fights for his freedom, and the protagonist helps him at first. Later, the protagonists understands, that his friend's (the antagonist's) freedom, comes in a price of millions of deaths. So he must choose the lesser of two evils - sacrifice his friend's freedom for the sake of many people, or sacrifice many people's lives to help his friend be a free man. A difficult choice.