Protagonist is born with a special talent because of his/her lineage. His/her parents may be keeping this secret from the protagonist, or they may be dead, or he/she may be adopted, or one parent may be absent, and the absent parent may have a special power or may otherwise be a stand-in for God. Of course, specialness can take on many forms, and doesn't necessarily involve superpowers, but generally, it does.
Protagonist discovers said talent when they come of age, and are initiated by a mentor or mentors. Protagonist discovers that he/she must use said talent against the forces of evil, usually one particular antagonist. Despite the awesomeness of their circumstances, the protagonist is at first reluctant to take on this new responsibility, but eventually they give in. They may be fulfilling some prophesy, or they may be the world's only hope. If the author has decided to just screw it and nail the point home by hitting it square on the nose, the protagonist will be referred to as "The Chosen One."
Usually the evil antagonist is exceedingly boring and lacks complexity. Usually wears a cape. May or may not be horribly disfigured. The disfigured are bad. The color black, is bad.
Insert love interest here.
When called upon to do so, the protagonist rises to the occasion, conquering the evil with not just their power, but their cunning.
Repeat for as many sequels as you can draw the sucker out for.
And no I'm not only talking about that book, the book that must not be named. I'm sure you can come up with at least a dozen others that follow the same pattern, even if you don't read young adult fiction. YA isn't the only guilty party. But seriously, I think we can do better.
What Would Jesus Do?
So Jesus starts out with circumstance number one, but rather than a stand-in for God, it's God himself. Then there are those missing years. Jesus may have had a mentor. Who knows? What we do know is that he had magic powers, but he didn't exactly use those powers to fight the forces of evil. Jesus mostly just talked a lot. He preached. He told people to be humble, and to be nicer to eachother. And what happens in the end? Does he conquer the forces of evil? Well, not exactly. The Gospels really aren't about the devil. It's a more complex, richer story for its ambiguity. It doesn't take the low road by presenting us with easy villains. People are flawed, and Jesus acknowledges that even he, is flawed.
There's your messiah story, but it's just not exciting enough. Where are the capes? Where's the love interest?
I'm not a religious person, but I will say, as messiahs go, Jesus makes for a more intriguing and complex messiah than Harry Potter, or Luke Skywalker, or any number of others.
No More Villains and Messiahs Please
It's harder to write a compelling story without a villain, but that doesn't mean it's impossible. You don't have to preach to your readers to give them something other than black hats and white hats. Your protagonist doesn't have to be Jesus or any other messiah. You can have all the spaceships and dragons you want--who doesn't like spaceships and dragons? But you can still rewrite the script. That doesn't mean eliminate conflict, but not all antagonists have to be quite so antagonistic. People are more complex than that. People are people. Villains are plot devices. So please, please, write something different. Your readers deserve it.