I think you are confusing being a protagonist with being a Mary Sue.
Nope. You don't know a lot about storytelling and narrative if you seriously think that a protagonist by definition has to be heroically good, capable and born-into-greatness by the token predetermined external explanations. I studied Joseph Campell in film school, and I can tell you with certainty, that Lucas developed Star Wars out of his blueprint of the Hero's Journey, and Luke is the definition of parcel fitted hero characters. He was written to be instantly good, relatable and likeable. He is a Mary Sue, and even when he fails he does it out of kindness. That is the traits of a Mary Sue character.
There are many protagonists who are written from a point of view, that has a lot more growth. It's a common tool in scriptwriting (and fiction in general) to write your protagonist to be very far in belief and state in mind from where they start. Luke is as good hearted at the end as he is in the beginning. He refuses the quest to adventure (Obis call for aid) but does the right thing anyway when his goodness based nature prevails.
There are many protagonists who doesn't work like that. A pivotal character change is not about physical power, it's also about what type of character they are. Are their beliefs and world views fundamentally different at the end of their journey than in the beginning? Sometimes you have characters who start out as cowards, or evil, or bad or wrong somehow. That's not the case with Luke at all, and he never fails himself. It's easy and convenient to write your characters as likeable, but it makes them less relateable in the end. Even though Luke is the hero of Star Wars, a lot of people are more fascinated with Han Solo and Darth Vader because their flaws make them more interesting.
And if you actually sit down and read Campbells works like the Hero with a Thousand Faces you can see that these dramaturgical fundaments have been used in story since the ancient greeks. In those stories you had all-powerful warriors and lords, but they often ended in tragedy due to character flaws of their own doing. Even when Luke is bested by the emperor physically in battle, he still wins because he doesn't give up (give in to the dark side). Its a pretty straight forward way of winning, even when you are losing.
I hate Superman because he is boring. His goodness, and kindness is boring. His powers are boring because he is born into it. That doesnt mean that Superman doesnt make mistakes. He does, and he has weaknesses (like kryptonite). That doesnt mean he is not a Mary Sue.
Batman is a much more flawed character and as a result more interesting. His power is not given to him in the same way, and he is much more on an equal footing as some of his enemies. It makes for better drama.
You can apply that to almost anything. Mickey Mouse is boring as shit for the same reasons. Donald Duck is an endlessly better character due to all his character flaws. He is short tempered, unlucky, a shitty uncle/nephew/boyfriend. He is lazy. He is jealous. He is so many bad things, and those flaws end up making much more compelling scenarios than mickey mouse, who is way to good and sweet and one dimensional. Mickey Mouse was written to be liked right off the bat. But thats easy and boring. Doesnt have anything to do with being a protagonist.
