The Star Wars franchise has always had at least one main protagonist for viewers to focus on. In the original trilogy, it was Luke Skywalker and his quest to become a Jedi. The sequel trilogy put its focus on Rey and her journey to discover her past. Even Star Wars Rebels focused on a larger ensemble but always centered around the show's youngest character, Ezra Bridger. While many of its properties have always had a way of centering the main story around one character, the prequel trilogy has remained an outlier.
Since the release of The Phantom Menace in 1999, the trilogy of films that set up Luke Skywalker's journey never appeared to settle on a true protagonist. Some fans believe that Anakin was the main protagonist, while others think it was Obi-Wan or even no one at all. There has never been a definitive answer to the theory, but there has been evidence accumulated from all three films that build cases for each possibility.
Anakin Skywalker
Aside from the fact that all of the main films in the franchise are dubbed the Skywalker Saga, The Phantom Menace set up Anakin's place as the main protagonist from the moment he stepped into frame. According to prophecy, his birth through the Force placed him in the role of the Chosen One, someone who would bring balance to the Force. Anakin was an immensely powerful Force user who was also an expert swordsman and pilot. Over the course of three films, viewers were able to see him grow, get married and struggle with his emotions that eventually led him on a path to the Dark Side. The prequel trilogy made sure to focus on the young hero and the decisions that led him to father Luke and Leia and help the Empire rise to power, making him a logical main protagonist.
Obi-Wan Kenobi
While Obi-Wan Kenobi wasn't the Chosen One, the prequel trilogy put him in a position that could be perceived as the film's main protagonist as well. From an emotional perspective, the films showed Obi-Wan as a young Padawan who was forced to train a young Anakin after his master Qui-Gon Jinn's death. The following films saw the two build a brotherly relationship that was shattered when Anakin fell to the Dark Side. The emotion and pain were felt solely through Obi-Wan as the audience stayed with him when he discovered Anakin's turn.
For a narrative standpoint, Obi-Wan was also present for the important moments that brought about the galaxy's most pivotal events. For example, Kenobi was the one that discovered the secret clone army on Kamino and followed the breadcrumbs to Count Dooku. His findings eventually led to the first battle of the Clone Wars, which marked the beginning of the end for the Republic and the Jedi. His story culminated in his exile on Tatooine, where he tasked himself with keeping Luke Skywalker safe from anyone who wished to do him harm. Obi-Wan's presence during the film's most important moments make him a perfect choice to be the main protagonist.
No One
With the Age of the Republic, there are many moving parts that the films kept track of. From the Clone Wars to the political tensions with Chancellor Palpatine and the Jedi, the possibility that there wasn't a main protagonist at all seems credible. The prequels' overall story was about Anakin's fall to the Dark Side and the Republic's collapse.
To properly tell those stories over three films, it became important to cover them from different perspectives, from Anakin and Padmé to Obi-Wan and the Jedi during the Clone Wars. As each character played their part in Palpatine's grand scheme, whether with Anakin turning evil or the activation of Order 66, it was too late for anything to be done to change the outcome. With so many characters and stories to follow, not singling out a main protagonist may have been the best course of action.
The prequel trilogy is all about changing what was and making something new. In this case, it was about the balance tipping to the Dark Side and the beginning of the Galactic Empire. No matter who the film's main protagonist was, the important thing was that viewers understood what happened and why the losses felt were so tragic for characters like Obi-Wan and Anakin.