I think part of the misunderstanding surrounding the Star Wars Prequel Trilogy lies in truly understanding the plot. It isn't obviously clear to all and that is quite deliberate. So, I will delineate the real story, including the goals that arc over the three films and show why limiting it to those stories was important.
Senator Palpatine of Naboo, secretly a the current Sith Lord who goes by the name Darth Sideous, has seen how corrupt the Jedi have become and how easy they can be toppled if that people of the republic where shown their weakness. To do so he must be in power. His first step is to work as Darth Sideous to get the Trade Federation to blockade his own world. Two Jedi are sent to investigate the blockage and get involved, chance landing them on Tatooine where they find a young boy who they believe is the Chosen One, a being prophesied to bring balance to the force. We see in the treatment of this boy and the Jedi who found him, that they Jedi have become closed and rigid, more concerned about following the code and the rules than in their purpose. Senator Palpatine successfully uses the situation to oust the Chancellor and take his place, but in the process he has lost his apprentice. He sees in young Anakin Skywalker the seeds of a new apprentice, but he is in the hands of the Jedi and not ready. Unphased, he begins sowing the seeds by becoming Anakin's mentor while Obi-wan Kenobi becomes his teacher and master.
A decade passes. In that time Palpatine has been busy. He has sown the seeds for a war that will rip the galaxy apart, put him in ultimate power, and destroy the Jedi. Whether through direct or indirect action, he commissions the cloners on Kamino to create a clone army for the Republic. At the same time Palpatine's new apprentice, Count Dooku, also known as Darth Tyranus, is leading a separatist movement with the help of the Trade Federation and their battle droids. Palpatine initiates the war when the Jedi uncover the clone army, forcing the Republic to adopt the army and put it to use. Palpatine uses his influence to have himself granted special powers to conduct the war.
He continues to make or take opportunities to fill Anakin's head with his own teachings in subtle ways. Anakin's unorthodox style is likely the direct result of his mixed Jedi and Sith teachings and he passes that style on to his own Padawan, Ahsoka Tano. The tale of the Clone Wars themselves fall outside the movies, but the emphasize what the real story is and were originally intended to be told in a movie.
When the movie story resumes we are shown a glimpse of Anakin and Obi-wan's antics during the clone wars. Palpatine has been kidnapped by Count Dooku as a stunt. Unfortunately Dooku doesn't realize that the war is about to come to an end and Palpatine has no further need of him. Anakin rescues Palpatine and, at Palatine's urging, executes Count Dooku. As the war winds down, Palpatine's plans come to fruition. He isn't about to give up his powers and implements the order he had planted in all the clones that turns them against the Jedi. He uses a confrontation with Mace Windu to turn Anakin to the Dark Side and then sends him first to destroy the Jedi Temple and then to kill the Separatist leaders. He blames the Jedi in the Senate and cements his power. By his actions he had changed the face of the galaxy and the Sith have finally won.