Here are the details on my PT.
Forgive me if it's a little long. =)
Episode I - The Beginning
Takes place about forty years before ANH, wih the Clone Wars already long underway. The specifics of the Clone Wars (such as who are the clones, who they fight for, etc.) are not revealed.
Lord Maul (no "Darth", just "Maul") is the main villain of the story. He hires the Neimoidians - a federation of mercenaries in my PT - to invade Naboo and exterminate the reigining royal family. He is a Sith Lord, but neither the Neimoidians nor the Jedi learn of this.
Padmé is a princess of Naboo, the middle child to the reigning King and Queen (no "elected queen" stuff here). Both her parents and siblings are killed by the Neimoidian forces. She has limited Force abilities, namely the ability to see glimpses of the future.
Palpatine's father is the Grand Vizier of the King and Queen.
Qymaen jai Sheelal (General Grevious) plays the "ANH Vader" role as the supreme commander of the Neimoidian droid armies, though he is not a cyborg in this story.
The Gungans are allies of the Naboo, and can speak English relatively well (fuck that broken pseudo-Jamaican patois). They place Padmé under their protection after her home is destroyed.
Obi-Wan is about twenty years old and has recently attained Knighthood after several years of tutelage under Yoda. He has been assigned to a team of commandoes - lead by Colonel Bail Organa - on a mission to rescue Padmé from the Neimoidians.
Qui-Gon is a sixteen year old apprentice who has not yet completed his training. With his master (Dooku) recovering from injuries incurred from an earlier mission Qui-Gon has been temporarily placed under the care of Obi-Wan.
Captain Tarpals assumes Jar Jar's role (if Jar Jar himself exists, it's as Boss Nass' retarded court jester).
Anakin is about fifteen years old, and lives on Tatooine with Shmi, Owen, and Beru on their moisture farm. He is a foundling, and has never known his biological parents.
Watto is portrayed much like he was in TPM, but is also a corrupt gangster. The Lars are deeply in debt to him. He also has no problem accepting Republic credits (they can just be exchanged :)).
No pod race (there's no need for one anymore).
There is chemistry between Anakin and Padmé, though no true romance blossoms between them at this time.
Dooku is introduced, but is only a minor character.
The Prophecy of the Chosen One is defined, fleshed out.
The history of the Sith and their (supposed) extinction is revealed.
Theed is nuked.
Maul is badly injured at the end, and is thought dead, but is he ...?
Nute Gunray dies.
Sheelal attempts to kill Padmé, but in a battle with Tarpals is killed(?) by an exploding thermal detonator.
At the end Padmé goes through her coronation and is crowned the new Queen of Naboo.
Episode II - Knights of the Republic
Takes place a couple years after Ep. I, in the final months of the Clone Wars.
It is revealed that the main antagonists in the Clone Wars are the Kaminoans, who are genocidal extremists obsessed with purifying the universe through genetic engineering and eugenics. The foot soldiers of the Kaminoans are clones, some of which were cloned from Force-sensitives. The Force using clone troopers wear white robes over their armour and weild yellow lightsabers.
During a parade Padmé is nearly assassinated, which leads to the Jedi Council calling Anakin and Obi-Wan away from the frontlines to protect her.
It is revealed that Padmé is no longer the true leader of the Naboo. The corrupt parliament - lead by Palpatine Sr. - has wrested control away from her and made her nothing more than a figurehead. The assassin who tried to take Padmé out was an emissary of a group of insurgents who are fed up with the corrupt government.
It is revealed that Commander Sheelal survived Ep. I and was recreated as a cyborg by the Naboo to serve as Padmés "bodyguard".
Palpatine Jr. - the future Emperor - is introduced. He's apparently a friend of Padmés who is sympathetic to the insurgent cause.
It is at this time that a real romance begins to bloom between Padmé and Anakin. Anakin chooses to resist his feelings due to the Jedi's rule against attachment, though, much to Padmés chagrin.
Anakin believes that he should help the insurgents overthrow the government, but the Jedi Council forbids it and Obi-Wan agrees with them, causing strife between the two Jedi.
Eventually Obi-Wan has to be called away on a mission to destroy a cloning facility on an enemy planet, leaving Anakin alone to protect Padmé.
Dooku returns as a supporting character. He joins Obi-Wan in the mission against the clones.
Anakin and Padmé side with the insurgents, and together they all overthrow the corrupt government. Palpatine Sr. and his cronies are arrested, and eventually put on trial and imprisoned.
Palpatine Sr. dies in prison, when a droid created in his son's image visits him in prison and explodes. The culpit is Maul (or is it?) who is revealed to have survived Ep. I.
Due to his actions, Anakin is kicked out of the Jedi Order. He and Obi-Wan part on good terms, and he returns to Padmé and Palpatine Jr. on Naboo to help the newly created government get on its feet.
Padmé then has a disturbing dream of Anakin falling to a black-cloaked figure in a lightsaber duel (ooohhh, ominous XD).
Episode III - A Lost Hope
Twenty years have passed since Ep. II. The Clone Wars are long over, and Palpatine is now the Supreme Chancellor of the Republic. Anakin and Padmé are now married and living on Coruscant, with Anakin serving as Palpatine's bodyguard. There is turmoil within the Republic, however. Palpatine's government is believed to be corrupt, and Dooku - once an esteemed Knight within the Order - has left and now leads the Seperatist movement in opposition to Palpatine.
Relations between Palpatine and the Jedi are strained. Many have defected and joined Dooku, with the Jedi Council members themselves remaining loyal to Palpatine only out of a sense of obligation to the Republic. Concerned that the Jedi may be conspiring against him, Palpatine places Anakin on the Council to keep an eye on them.
Eventually Dooku attacks Coruscant and captures Palpatine. Anakin and Obi-Wan reunite, and go to rescue the Supreme Chancellor. After infiltrating Dooku's ship, cutting through Dooku's Jedi acolytes, and making their way to the bridge they engage Dooku in battle. It is there that it is revealed that Dooku is aware that Palpatine is in fact a Sith Lord, and plans to kill him. Believing that Palpatine is the only one who can restore order to the galaxy Anakin slays Dooku.
Obi-Wan eventually reveals Palpatine's secret to the Jedi Council, and it is then that they decide to rise up against Palpatine. When a contingent of Jedi led by Mace Windu is sent to arrest him, though, Anakin engages and defeats them. It is then that Palpatine decides the entire Jedi Council is against him. Anakin is sent with a battalion to the Jedi Temple, where they wipe out most of the Jedi stationed there (young children are spared and taken away for "de-programming").
It is revealed the Maul is not the one who had Palpatine Sr. killed, but Palpatine himself. Both Maul and Palpatine served as his apprentices, and Maul was completely devoted to his master. With eleven of his own apprentices, Maul attempts to avenge his slain master, but Palpatine is able to slay them all.
Yoda and Obi-Wan are among the few Jedi who escape the razing of the Temple, and together they reveal to Padmé Anakin's fall to the dark side. The three realize that the Sith must be stopped. Yoda himself believes that Anakin is completely corrupted and must be killed along with Palpatine, while Obi-Wan and Padmé both believe Anakin can be saved.
Padmé goes to Anakin and tells him that Yoda and Obi-Wan are hiding on Mustafar. Anakin reveals this information to Palpatine, who decides that they will journey to Mustafar together to take out the fugitives. Once they arrive Palpatine assigns the task of taking out Obi-Wan to Anakin, choosing to deal with Yoda himself.
Anakin finds Obi-Wan and the two duel. Obi-Wan holds back, trying to persuade Anakin to reject the dark side, but Anakin refuses. In the end Anakin loses his hand to Obi-Wan and he falls into a river of lava.
Palpatine himself tracks down Yoda, and sends his Royal Guards to take him out. After Yoda defeats the Guards Palpatine engages the Jedi Master himself. The two are too evenly matched, and their battle ends in a stalemate.
Anakin, having used the Force to protect himself, survives his fall into the lava, but is covered in burns and has lost his legs and lower torso. Palpatine finds him, and together they leave the volcanic world.
Yoda and Obi-Wan leave Mustafar and reunite with Padmé. They learn that Padmé is pregnant, and it is decided that she must leave Anakin and place the children under protection once she gives birth.
Palpatine has Anakin rebuilt as a cyborg. Palpatine reveals to him that Padmé has disappeared. The fallen Jedi is at first enraged, realizing that she betrayed him, and then falls into despair, admitting to himself that he has no one but himself to blame for her departure.
Months later Padmé is now living on Alderaan with Bail Organa and his wife, having had her face and voice surgically altered. She gives birth to the twins Luke and Leia. It is decided that Leia will remain on Alderaan, to be raised by the Organas with Padmé as her caretaker, and with Yoda taking Luke with him to Dagobah (a series of events take place between Eps. III and IV which leads to Luke being relocated to Tatooine to live with his stepuncle).
Palpatine officially reorganizes the Republic into an Empire, and he and his apprentice Darth Vader are left with the task of dealing with the leaderless Jedi left scattered across the galaxy.
Miscellaneous
The Jedi number in the billions. Though the Jedi Council is stationed on Coruscant there are countless other Jedi academies and training centres established on other worlds.
The Jedi wear all-black uniforms, similar to Luke's outfit in ROTJ, except for very young trainees and initiates, who wear all-white.
The Jedi weild only blue (azure) lightsabers, and the Sith weild only red (crimson) lightsabers; the only exceptions are : Anakin, who weilds a cyan lightsaber; Jedi initiates, who weild white training sabers; and Asajj Ventress, who weilds one deep blue lightsaber and one green lightsaber (I didn't bother mentioning her in my synopsis since she's essentially a peripheral character).
Yoda doesn't carry a lightsaber. He carries a tall white staff, which he can make lightsaber-resistant with the Force.
Palpatine doesn't carry his own lightsaber. When he chooses to use a lightsaber (which he rarely does) he just takes one from an opponent.
Palpatine is actually younger than Anakin and the other main characters. His nasty appearance in ROTJ is the result of decades of being eaten away by the dark side.