In Legends, Sidious encouraged Vader to hunt down the remaining Jedi, including Obi-Wan and Yoda. He was concerned about the potential havoc those remaining Jedi could cause, and wanted them out of the way. They weren't discovered because they both chose good hiding places.
So in the end, Palpatine was content with his victory over the Jedi and felt it pointless to personally hunt down Yoda out of revenge. Although, there's no doubt that Palpatine would've liked to have killed Yoda himself.
Mace Windu failed in his mission to arrest Palpatine in Star Wars: Episode III - Revenge of the Sith, but Yoda may well have fared better. As powerful as Darth Sidious may have been, it's easy to forget he actually seemed afraid of Master Yoda.
Palpatine admits to Darth Vader that the Jedi he actually feared most was none other than Jocasta Nu.
Why Qui-Gon Jinn Was Palpatine's Greatest Threat. Unlike Yoda and the Jedi High Council, Qui-Gon Jinn was only concerned about the will of the Force. Therefore, Palpatine needed Qui-Gonn out of the way because he was better connected to the Force than the other Jedi.
And while Yoda and Palpatine both worked with the Senate, they treated each other with the utmost respect. While Palpatine plotted in the shadows and planned his Galactic Empire, he underestimated Yoda. And even when Yoda discovered Palpatine's true nature, Yoda underestimated his power.
Palpatine Was Born With a Weak Connection To The Force
The reason why the Jedi might not have discovered Palpatine's Force sensitivity in Star Wars canon might be that Palpatine lacked an intrinsically-strong connection to the Force.
Palpatine's ability to sense the future probably helped a great deal to stay hidden from the Jedi Order. He was extremely talented at sensing the future and seeing the different paths ahead, so he could easily predict multiple outcomes and avoid ones that led to the discovery of his true identity.
Yoda didn't specifically know how this would go down, or to what degree Anakin would cause it to happen, but he was playing a much longer game by Revenge of the Sith, and that's at least, in part, explained by Yoda's Force connection with Qui-Gon's spirit.
During Palpatine's reign as Emperor, his apprentice's true identity was kept a secret, leaving only a few Star Wars characters aware Anakin was Darth Vader. Besides Obi-Wan, Master Yoda also knew the truth, as well as Ahsoka Tano, R2-D2 and C-3Po, and even Senator Bail Organa.
Arguably, Qui-Gon is wiser in some ways, given that he knows how to preserve his consciousness in death. Yoda is wise, but sometimes flawed, given that some of his views align with the problematic thinking of the Jedi of this era.
The Skirmish in the Senate was a confrontation that took place in 19 BBY between the Dark Lord of the Sith Darth Sidious and the Jedi Grand Master Yoda. The two veterans of the Force engaged in a ferocious lightsaber duel, with each making liberal use of their powers.
The novel details Plagueis betraying and overthrowing of his own master Darth Tenebrous; his work as head of a powerful banking consortium on the Muun homeworld; his discovery, recruitment, and training of the teenaged Palpatine of Naboo; and the efforts of Plagueis to undermine the Galactic Republic and ensure the ...
Palpatine, as a Sith Lord, despised the Jedi's adherence to strict codes and their perceived limitations. He viewed their commitment to selflessness and detachment as weak, believing that true power could only be achieved through embracing strong emotions and personal desires.
There, he discovered Anakin Skywalker, a boy with enormous strength in the Force. Qui-Gon believed Anakin was the Chosen One, prophesied to bring balance to the Force, and that their meeting was no accident.
Palpatine Never Truly Thought Highly Of Darth Maul
Darth Maul died during a final battle with Obi-Wan in the Rebels TV series, and Palpatine couldn't have cared less. For him, finding and killing Maul for his failure simply wasn't worth the effort.
Obi-Wan discovers that Qui-Gon's old master, Count Dooku, has become a Sith Lord; and Dooku mentions Qui-Gon as he interrogates a captured Obi-Wan, expressing grief over his former apprentice's death and debating that Qui-Gon would have followed him in leaving the Republic had he survived.
But one Jedi stands above the rest and needs to start getting recognized as the greatest Jedi who ever lived. That is none other than Obi-Wan Kenobi. While this saga is ultimately the story of the Skywalkers, Obi-Wan is arguably the best and most pure Jedi to ever come out of it.
#1 – Yoda. Yoda is widely considered to be the greatest Jedi of all time, and with good reason. He is a master of the Force, a skilled warrior, and has an unmatched wisdom that comes from centuries of experience.
Padmé was well aware that Anakin had committed dark crimes that would've started his fall to the dark side. He even confessed to her that he had massacred an entire Tusken Raider village to avenge his mother, leaving no one alive.