Aside from being the main character, the protagonist is also often considered to be the hero of the story, the conventional "good guy." Thus, it's easy to say that Nel might be considered the real protagonist of the story, as she is presented as the "good guy," the one who is kind and obedient and doesn't hesitate to meet the needs of those around her, while Sula is often seen as the "bad guy." In the end, when Nel realizes that her personality is actually nothing more than a façade—a mask that hides her selfishness and hypocrisy—Nel experiences a major character's transformation, as she finally understands that she allowed herself to neglect her own real needs and desires to please others and be whoever they expected her to be.
Her experiences also make her very relatable, and readers might feel that it's easier to empathize with Nel rather than with Sula. In this sense, many might think that Nel's realization about her identity and, most importantly, her character transformation complete her and ultimately define her as the real protagonist of the story.
However, it is important to remember that Nel wouldn't have discovered her true self if it weren't for Sula; without the friendship she has with Sula, which is the focal point of the story, Nel would've never gotten the chance to allow herself to be who she really is. When she finally understands that she's just as "bad" as Sula, or rather just as human as Sula, she also realizes, albeit a bit too late, that Sula was actually the only person in her life that liked her for her, despite all of her flaws and imperfections.
Nel experiences her grand character transformation because of Sula and the relationship she has with her. She goes to visit the dying Sula, still upset with her, but leaves a changed woman—one who greaves not just the loss of a rare, beautiful friendship, but the loss of freedom and happiness as well, and it's all because of Sula's words of wisdom:
"You think I don't know what your life is like just because I ain't living it? I know what every colored woman in this country is doing."
"Dying. Just like me. But the difference is they dying like a stump. Me, I'm going down like one of those redwoods. I sure did live in this world."
"Really? What have you got to show for it?"
"Show? To who? Girl, I got my mind. And what goes on in it. Which is to say, I got me."
"Lonely, ain't it?"
"Yes. But my lonely is mine. Now your lonely is somebody else's. Made by somebody else and handed to you. Ain't that something? A secondhand lonely."
It's also noteworthy to mention that Nel is not fully transformed; she simply comes to the realization that the she has wasted years of her life neglecting her true self, trying to make everyone else happy, and her full character transformation is yet to come. She still has a lot more to learn, both about herself and the environment, and a lot more to experience.
Sula, on the other, remains true to herself, even at her death-bed. She has no regrets about her life, even though she accepts the fact that she actually lived a tragic life. She is not the "bad guy," but she is often blamed for everything and generally disliked by the community not because she's not good or moral, but because she dares to be who she really is—a proud Black woman, who is capable of making her own decisions and pursuing her own happiness, not caring what everyone else thinks about her. She refuses to conform and embraces her rebellious nature with no hesitancy. This is what makes Sula the typical misunderstood heroine—the one who unapologetically lives her life, constantly searching for her purpose and defining her identity along the way.
Sula is essentially what Nel and every other woman in the community is afraid to be throughout the entire novel. Nel may be the one who transforms, but it is Sula that reminds readers that no one in this world is only "good" or only "bad." Human nature is complex and multidimensional, and humans are multifaceted creatures that are capable of loving and hurting others, both consciously and unconsciously, and sometimes even at the same time. One might even argue that we're all both the heroes and the villains of our life stories.
In this context, it's more accurate to conclude that Nel is not actually the real protagonist because she is the one who is transformed in the end. Sula and Nel are simultaneously both the protagonists and the antagonists of the story—they're the "heroes," but they're also the "villains," as they learn how to accept themselves and their true identities in their own ways.