With their destinies already decided, a lot of the good decisions made by the main characters in the Star Wars prequel trilogy acted as foundations laid in place for the future. With this, some of the character's best choices came into effect later, but there were others that had more immediate positive effects.
While the effects of Obi's choice to stay on Tatooine wouldn't be realized for years to come, as shown in the trailer for the Obi-Wan Kenobi Disney+ show, there were other decisions made that allowed for early victories for the heroes of the trilogy. Whether selfless or self-serving, each character made at least one good choice.
Jar Jar: Staying With Qui-Gon And Obi
However a controversial character he may have been, Jar Jar did make one good decision throughout the prequel trilogy, when he chose to stay with Qui-Gon and Obi-Wan at the beginning of The Phantom Menace. After being exiled by his people, Jar Jar ended up owing a life debt to the Jedi, but had already chosen to stay with them anyway.
Jar Jar's insistence on accompanying the Jedi changed his life for the better. Not only did he help to bridge the peace treaty between the Gungans and the humans of Naboo, but he also became a Senator and close friends with Pé, which was a remarkable turn of events for his character.
Bail: Adopting Leia
Whilst Luke got sent to Tatooine to be raised by his Aunt and Uncle, Leia was adopted by Senator Organa and his wife, and it was certainly Bail's best decision throughout the prequels. Bail already wished for a child, and adopting Pé's daughter was a heartwarming notion, especially when considering how courageous Leia would be raised to be.
Out of all the tragedy of Revenge of the Sith, the adoption of both Luke and Leia at the film's conclusion gave fans hope, and Bail's decision to take in Leia was a touching tribute to his fallen friends. As audiences already knew, Leia would grow up with all of her mother's courageous spirit and political prowess, which may not have happened without Bail's moving decision to adopt her.
Dooku: Fleeing The Fight Against Yoda
Dooku was one of the best villains in the Star Wars prequel trilogy, but it seemed that even he knew went to retreat, as he did at the end Attack of the Clones. After expertly subduing both Anakin and Obi-Wan, Dooku faced Yoda in a duel that, for the most part, was evenly matched.
However, Dooku was wise enough to know when to accept defeat, however temporary he knew it would be. Knowing that Yoda's forces had already arrived on Geonosis, Dooku made the decision to flee the planet and leave the Jedi behind. In doing so, Dooku avoided capture (or even worse, death) and it was a smart move to make.
Mace: Bringing Backup To The Battle Of Geonosis
Mace's best decision in the prequel trilogy came in Attack of the Clones, when he led a strike team to the battle of Geonosis to confront Count Dooku. Mace's original intention was to question Dooku about his new droid army, but the decision actually led to Mace helping Obi, Pé, and Anakin to escape.
While the Jedi were initially overwhelmed by Dooku's army, Mace's decision to bring a team of Jedi ensured their survival until Yoda arrived with the Clone army. Despite it not being his actual intention, Mace's choice ultimately helped to save the main trio and showed the separatists that the Jedi were not to be messed with.
Qui-Gon: Saving Anakin
Despite only appearing in one film in the prequel trilogy, Qui-Gon stole the show in The Phantom Menace, and his presence was felt throughout all three films. He was a comionate Jedi who truly cared for those around him, and his decision to save Anakin from his life of slavery on Tatooine was his best one.
While Anakin's arrival at the Jedi order would eventually result in its downfall, Qui-Gon's decision still stands as a good one, as the fate of the Jedi and Anakin may have been different had Qui-Gon not been killed. Despite this, Qui-Gon's choice reflected the more favorable aspects of the Jedi and saved a boy who was in need, therefore securing it as the right thing to do, no matter what the consequence was in the future.
Yoda: Ordering For The Jedi To Hide
By the conclusion of Revenge of the Sith, Yoda knew that the time for fighting was over, and the best thing he could do was to exile himself, and for the remaining Jedi to go into hiding. The decision itself proved to be the right thing to do, as they couldn't risk being found by the newly formed Empire.
By taking himself away, Yoda's decision meant that he would eventually be found by Luke Skywalker, and thus the catalyst in the destruction of the Empire would be born. This choice within the trilogy may have seemed an act of defeat, but Yoda's guidance ensured the survival of the remaining Jedi, most notably Obi-Wan, who would be key in the downfall of the Empire, and therefore it was a wise choice to make.
Palapatine: Manipulating From Within
Master manipulator and clever strategist, Palpatine was the most intelligent villain in Star Wars for how he controlled those around him and bent them to his will. His best decision throughout the prequel trilogy was the choice to antagonize both parties in the war, and manipulate those around him whilst hiding in plain sight.
Close friend and confidant to Anakin, Palpatine expertly played on the young Jedi's weaknesses to ready him for his fall to the dark side, and he similarly exploited Count Dooku. Palpatine orchestrated the fall of the Jedi and the Senate, all the while keeping up the appearance of being their friend. Subsequently, his best decision created destruction for everyone else, but it furthered his cause perfectly.
Pé: Making The Peace Treaty
Even from a young age, Pé was extremely intelligent and understanding of the political landscape she had been thrust into, and she tended to be one of the more sensible characters throughout the prequel trilogy. Outside of her secret marriage to Anakin, Pé consistently made good choices, but her best came in The Phantom Menace.
With the threat of war hanging over them, Pé ordered a peace treaty between Naboo and the Gungans, and suggested they work together against the Trade Federation. Although Pé made many good moves as both Queen and Senator, especially throughout The Clone Wars, this was her best in the prequels - not only did her plan work, but it also showed off her adept political abilities immediately.
Obi-Wan: Staying On Tatooine
Regardless of all the heartbreaking things that happened to Obi-Wan, he still acted with comion and bravery, and his decision to stay on Tatooine to look out for a young Luke at the end of Revenge of the Sith reflected this. Forced into hiding by the rise of the Empire, Kenobi fled to the desert planet to take Luke to his Aunt and Uncle, and he chose to stay there.
With nowhere left to turn, Obi's decision to stay on Tatooine proved to be his best. It ensured that he would be able to keep an eye on Luke, and would eventually have the means to train him in the ways of the Jedi and help to bring down the Empire. Throughout the whole trilogy, this option held the most promise for Obi after all of the tragedy.
Anakin: Making C-3PO
Considering the path he was on throughout the films, it's no surprise that Anakin's best decision was on a smaller scale than the other, more wayward decisions he made. As a child in The Phantom Menace, Anakin made the protocol droid that fans had already come to know and love, C-3PO.
The decision was initially made to help his mother with household duties, but the outcome ended up far greater, with C-3PO becoming a fixture within Pé's escort and part of the Rebellion and Resistance in the years to come. C-3PO, however exasperating he could be, proved to be a vital character with his vast knowledge.