This thread reminds me how difficult it is to fit Anakin's story established in the OT into 3 films.
The first film sets everything up. It's the New Hope of the series. We don't really explore too much into depth of the characters. We just want to have a solid, action-based film that sets up the impending doom of the Clone Wars and establishes Anakin as a likable character.
The second film should focus on character development. The Clone Wars should be in full force and the characters should face tribulations. I think it's too early to have Anakin turn to the dark side in this film. We've only begun to explore the aspects of his character in this film, and it would be so sudden we can't sympathize with it. He should still be tempted and confused however. Of course, this is the film where Anakin and Padme develop a relationship. Perhaps Padme realizing she was pregnant would be good cliffhanger ending.
Based on this idea of the first two films, here is my vision of the third:
Anakin has been sent to battle on a far off system, and he has not heard anything from Padme or about the birth of his child. He is then greviously injured at the start of the film (not yet requiring a suit however, perhaps some facial scars, amputated arm, etc.) His driving motive is to get home to see his child and end the atrocities he has experienced in the war.
He comes back to Coruscant after Palpatine offers him a position to be his bodyguard and liason to the Jedi. Eager to leave the front lines and help end the war, he gladly accepts. However, as he is returning, he learns that Alderaan has been taken seige by the Separists, where Padme and the children were guests of the royal house. He soon has dreams of troopers gunning down Padme holding a child. The dream ends with Obi-Wan looking over her body. Anakin resolves to go to Alderaan to save his family.
Palpatine warns him to stay on Coruscant, where they discuss their mutual desire to end the war. They both agree that a more authoritarian republic could have prevented the war.
Palpatine also insinuates that the Jedi started the war and that they are planning to overthrow him. Given that the Separatists are lead by a former Jedi, this does not seem implausible to Anakin. The Jedi have treated him like cannon-fodder so far, so Anakin severely questions his loyalty to the Jedi. Not wanting to offend his friend, Anakin never talks about his misgivings with Obi-Wan.
Meanwhile, the Jedi assign Obi-Wan on a secret mission to Alderaan to kill Dooku. He is also charged with protecting the royal family. Anakin pleads to go on the mission so he can save his family, but the council denies him. Especially vocal is Mace Windu. Windu has always been suspicious of Anakin since he joined the Jedi. Though not expressing it to Anakin, he senses the growing cloud of darkness around Anakin and thinks he would be dangerous for such an important mission. Anakin becomes furious. He suspects the Jedi are covering their involvement on both sides of the war.
It is then that Palpatine reveals his true Sith identity. He pleads Anakin to leave the Jedi. He tells Anakin the Jedi council has become irreparably evil, and that the only way to end the war and save his family is to destroy the Jedi. Only through the dark side can he attain the abilities he needs to take down the evil council members responsible for the war.
Anakin does not give in yet. He goes to the Jedi Temple to meditate, but discovers the council has mysteriously adjourned. Assuming the council has gone to overthrow Palpatine, he rushes back.
There he discovers Windu about to slay Palpatine. He engages Windu in a scene reminiscent of Vader and Luke crossing sabers in ROTJ. Channeling the darkside he defeats Windu as Sidious goads him on. Anakin kneels before Sidious and becomes his new apprentice.
On Alderaan, Obi-Wan kills Dooku, but not before he reveals his involvement with Sidious. He reveals that Palpatine has ordered a squadron to kill Padme and the children. He rushes to go save them. He arrives just as the troopers begin their attack. The troopers burst in a room. Padme manages to hide Leia, and holds Luke as she is shot. The troopers radio in that she had been killed. Just then, Obi-Wan arrives and slays the troopers. He discovers Luke still alive under her mother and Leia hiding. Palpatine is not certain that the child is dead. Nevertheless, he informs Anakin that Obi-Wan lead a strike on the royal palace that killed Padme and his child. Anakin is furious with Obi-Wan, as Palpatine goads that even friends can betray one another.
Palpatine gives Order 66. Anakin personally tracks down Obi-Wan, who has escaped to Mustafar. They duel, and Anakin's fate is unclear.
Closing scenes: Palpatine announces the betrayal of the Jedi and the new Empire. Suited Vader storms the Jedi Temple. Leia stays at Alderaan, while Luke goes to Tatooine.