I always thought Sprout was the shonen protagonist. He’s not the smartest, he’s not the bravest, so he has to work harder than everyone else just doing simple things. He wants to be hokkage (sheriff) some day and he always screws up but he never gives up.

Shonen protagonists always have aspirations. They want to achieve something and they work hard for it despite their limtations. Sprout and Sunny have a lot of similarities like standing up for what they believe. The problem was, the moment the narrative morphed to favor Sunny, she forfeits the shonen protagonist tag.

“Doesn’t matter what the press says. Doesn’t matter what the politicians or the mobs say. Doesn’t matter if the whole country decides that something WRONG is something RIGHT. This nation was founded on one principle above all else: the requirement that we stand up for what we believe, no matter the odds or the consequences. When the mob and the press and the whole WORLD tell you to move, your job is to plant yourself like a tree beside the River of Truth, and tell the whole world — ‘No, YOU move.’” – Captain America

Both characters did this but only one was favored by the narrative. Shonen protagonists don’t gain favor from the narrative. They earn it. That’s their trope. Sunny lucked out that the events favored her because of Izzy’s actions. But if she decided to go visit another pony town and bring back a unicorn or pegasus with her to move the story along as opposed to just protesting at Canterlogic every year, I’d say she would’ve earned the narrative’s favor rather than it being given to her on a silver platter, keeping her a shonen protagonist.