I would say the fact that you choose a fascist dictatorship makes it cliché, it is too close to the Holocaust and reminiscent of Hitler exterminating the Jews, Gypsies, Homosexuals, etc. No matter what you do, the "fascist dictator" will be equated with Hitler, your "mutants" will be equated with Jews, your "extermination" will be equated with concentration camps, gas chambers, etc.
Not only that, but you will invite terrible comparisons: Because of the obvious parallels to the Holocaust, the first question of any critical eye (including agents and publishers) will be; Is the hidden message of your book that Jews (or Native Americans) are the equivalent of "mutated humans"? Flawed humans? Sub-humans? Worthy of hatred because they are ugly or different? Is this a metaphor for race? Or homosexuality?
IMO, in the current political climate of the world, that makes this book very difficult to write; the mutants have to be unequivocal heroes and the government unequivocally evil and the non-mutant citizens mostly disagreeing with their government; because readers are going to identify with those non-mutant citizens, or the mutants being oppressed. Those dynamics will apply to ANY book discussing discrimination based on appearances, which is what I worry you are aiming toward. And that, in turn, can make your story seem predictable and cliché, unsurprising and lacking depth.
Your better bet is along the lines of Avatar, in which the villains are powerful but motivated to evil by the profits to be had by taking the alien's land to mine. One could say much the same about Native Americans; their extermination was in large part a war of conquest for their territories. Subtract racial motives and the government, and you have Avatar.
Greed is and will always be an understandable motivating factor.
I think much of your story line can be the same, but I'd rethink what you are trying to do. I wouldn't make the reason for discrimination a visual difference or religion or beliefs; those are too reminiscent of the Holocaust. For the same reason, I'd ditch the Fascist Government (no matter what you think Fascist means, to most people it means "Hitler"), and go with some other motivation. Perhaps by corporations. Perhaps it isn't the government doing it, but the government is weak and underpowered, or even non-existent.
A Dystopia is generally (even in the Hunger Games) a situation in which "good" civilization has broken down and cannot protect any citizens from predation; it is humans in the wilderness without resources and subject to predation and lethal conflict from all sides. Nobody is safe. Everybody has to be self-reliant to avoid being prey to other humans.
The heroes become the good vigilantes and/or law enforcement or saviors that risk their lives for others: Clint Eastwood in Pale Rider. An old west tale, a rich guy hires mercenaries to terrorize gold miners into giving up their claims; gunslinger Clint happens to be in the area and fends off these attacks, but the rich guy escalates and -- Right prevails, then Clint rides off into the sunset.
If you think about it, these are metaphors for the dream (or fantasy) of "good government" protecting the weak from the strong (instead of catering to the strong).
Now some might say that is itself a cliché, but I'd say it doesn't matter. Readers (and thus agents and publishers) like happy endings, they outsell unhappy endings 10 to 1. It is also okay to take inspiration from the Holocaust, but it is not a good idea (if you want a lot of people to enjoy your writing) to make this too obviously a retelling of the Holocaust.