Obi-Wan Kenobi (Ewan McGregor) was always the biggest threat to Palpatine's (Ian McDiarmid) plans in the Star Wars saga, even though Yoda was ranked as Grand Master on the Jedi Council. Kenobi's experience, personality, and relationships formed him into one of the wisest and most skillful Jedi in this franchise. Throughout the prequel trilogy, Obi-Wan always found himself face to face in situations that were a part of Palpatine's plan to create a new Empire, and proved a constant thorn in his side.
Yoda was an intelligent Jedi who contained many skills and knowledge revolving around the ways of the Force. He even fought Palpatine one-on-one towards the end of Obi-Wan never battled Palpatine in the movies, he was always an obstacle to his schemes.
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Why Even Obi-Wan Couldn't Stop Palpatine
While Obi-Wan Kenobi was Palpatine's true threat throughout the course of the prequel trilogy, Palpatine always had the upper hand. With an army of clones under his wing, control over the Senate, and powers stronger than anyone could imagine, the Emperor was always so far ahead that even Obi-Wan couldn't stop the Dark Lord. The Jedi did cause some bumps in the road for Palpatine by defeating Darth Maul, vaguely learning about his plans, and trying to bring back Anakin. That's more than Yoda ever did throughout the trilogy. Still, Kenobi's warm heart and powers were no match against Palpatine.
Obi-Wan Kenobi played a major role in trying to stop Palpatine's plans, whereas Yoda didn't do a lot physically despite his fight against the Emperor. Kenobi's training and wisdom were a powerful combo on-screen and almost allowed him to foil Palpatine's plot against the Republic. Consequently, he was always the true threat to Darth Sidious.
