Are you focusing on the Clone Wars?
Yes. The initial outbreak of conflict in the war makes up the plot of the first film. The worst struggles for the Republic make of the story of the second movie, while the last prequel features demonstrates how the war ended, and the immediate aftermath of it on the Republic.
Who are the Clones?
The clones are specifically those of various criminals, pirates, and various disenfranchised peoples from systems in the Outer Rim.
How does the War pertain to them?
They are initially recruited and later led by a remnant of Mandalorians who do an initial attack on the Republic in the first film, and shortly afterward start a full fledge invasion.
How does Cloning become irrelevant by the start of Episode 4?
Various cloning facilities are purposefully destroyed or sabotaged by the clone armies to prevent the Republic from learning how to replicate them, with Mandalorian leaders being the few who genuinely know the specific nature of the process. What materials and science the Republic forces are able to get their hands are confiscated and end up in the hands of those loyal to Palpatine, who's hinted at keeping and potentially utilizing the technology himself.
How is cloning limited to the point that the whole story doesn't get consumed by the idea of clones replacing major players?
Both cloning and providing weapons/ships to individual clones take a great deal of resources to do. Mass production of clones (necessary to get the amount of armies necessary for an invasion of the Republic) leads to ones not as healthy, intelligent, and resourceful as natural people. The invading fleet relies largely on sheer numbers for a long period. The gradual whittling away of resources needed to create clones destroys the numbers of the Mandalorian Coalition.
Are the main characters soldiers in the War?
Kenobi and Anakin both serve in high positions, technically serving under Republic Supreme Admiral Bail Organa. (Bail later retires from military service in favor in public office as the war winds down).
Who are the armies?
The Republic has a large unified fighting force of conscripted citizens of systems, and paid officers, many led by specifically by the Jedi, though some infighting between various planetary groups does hamper initial Republic efforts. The Coalition forces are more loosely organized, with massive units commanded by Mandalorian leaders, with the original Outer Rim soldiers underneath, and the clones serving as raw infantry.
Who is the larger force?
The Mandalorian Coalition initially outnumbers the Republic forces, but are gradually whittled down to resistance units by the end of the war.
What are the objectives of both sides?
The Coalition simply wants to take over the galaxy, with a specific aim of defeating the Jedi. The Republic is simply defending itself and aiming to imprison or eliminate the Mandalorian leaders, while containing the clone threat.
When did/does the War start?
A series of odd and unknown attacks/skirmishes take place on the outskirts over a year or so, initially thought to be raids by criminal gangs and pirates. The first major attack occurs roughly 26 BBY, the time of the first film. Jedi and Republic forces are able to beat invaders back, its soon realized that many, many more will be coming soon enough. The initial smaller encounters are later referred to as the First Clone War, with the major battles several months afterwards seen as starting the Second Clone War.
How does the War end?
Republic forces are able to wear down the Coalition and destroy their cloning resources over time. Many non-Mandalorian soldiers end up outright surrendering and/or deserting the cause, and end up anonymous on various Republic planets, an action freely condoned by Palpatine who states that such loss in numbers will end the war sooner. Some express concern at this, noting that large numbers of unlisted people in the Republic unable to get real employment, will likely turn to crime. (Its suggested that the amount of illegal spice trade, smuggling, bounty hunting, and slave trafficking will skyrocket soon enough)
The Mandalorian leaders finally agree to a ceasefire and put forth negotiations for their surrender via an initial treaty. The Jedi, distrustful of Palpatine, keep the conference a secret temporarily to prevent his interference. Both groups are destroyed when Palpatine (given the location by Anakin) orders his secret forces to destroy the station their where the negotiations are taking place. Palpatine deceives the Senate and explains that the Coalition double crossed the Jedi and that secret Mandalorian sympathizers will be taken care of, a move he uses to wipe out any remaining Jedi he can locate.
Do you show Obi-Wan receiving training from Yoda?
No, though the former mentions several aspects of his own training and specifically what he's passing on to Anakin.
Do you show Anakin receiving training from Obi-Wan?
The latter half of the first film and first act of the second film show Kenobi training him. In a contrast to Luke, who's questions and learning applied to the nature of the force, Anakin with his intuition picks up those aspects quickly and his education lies more in the application and temperance of the Force's use.
Are Obi-Wan and Anakin friends? When do they have the chance to establish this friendship?
The two are very close, gaining a kinship shortly after they first meet. The two in fact complement each other quite well, with Kenobi in fact being the more playful, laid back mentor in contrast to Skywalker's more serious minded student. Anakin almost always refers to him as "Ben" and sees him as an supportive older brother. While initially approaching each other with some reluctance in the opening act of the first film (Ben seeing Anakin as a bit too intense, and Skywalker seeing him as too lax) they grow over the film as friends with their mutual dedication to justice and peace.
How many years before Episode 4 does your story take place and how old are the main characters?
The first film takes place about 25 years prior to a New Hope. The second film is two years afterwards, and the third film three years after that.
Will you show Yoda?
Yes, but he appears gradually as the trilogy goes on. Viewers see only his face in the first movie, and his actual size isn't demonstrated until Anakin finally meets him in the second movie. While seemingly aloof and distant initially he becomes warmer and kindlier over time. He acts somewhat similar to Kenobi in the original films, as a wise mentor to both Ben and Anakin. He is the Jedi with the most awareness of how troubled Skywalker is, though even his does not know to what degree.
Will you show that Luke has a twin sister? Named Leia?
Yes. In the third film Anakin and Ben initially believe that Mother Skywalker and her unborn child are killed in a attack in the war. This tragedy eventually drives Anakin to be tempted by the Dark Side and the power of Palpatine. Following his turn and injury in the lava pit, Kenobi, Yoda, and Bail Organa discover that Mother Skywalker is alive, with two healthy young twins. The attack did however do damage do her during birth, and she's given less than a year to live. She goes with to Alderaan to live out her final days with the soon to be adopted Leia, and Kenobi promises that he will watch over Luke at Tatooine.
Will you reveal that Anakin becomes Darth Vader?
Yes. Darth Vader in terms of theme and metaphor really exists as the darker, more cynically pragmatic part of Anakin's psyche that grows as the Clone Wars go on. The battle for his soul begins to appear in the second film and takes center stage in the last film. The turn to the Dark Side signifies Vader's victory and the ruthless actions afterwards signifying the betrayal of Skywalker's compassion and empathy.
Will you have surprises in your new PT? Will it affect anything that we thought we already knew in the OT?
Not really surprises, as much as playing with expectations of characters. Even though Anakin is the one who eventually turns, he comes across as a bit more likable than Ben at times. Because "Sidious" as a concept does not exist, Palpatine appears initially as a weak willed populist dismissed by most as being easily manipulated by others. Darth Vader, rather than a literal person or simply what Anakin becomes, is more of a internal dark voice within Skywalker. The nature of the dirty "used future" in the galaxy is demonstrated to be a result of the Clone Wars and its aftermath. The prequels really serve to demonstrate how different the galaxy once was.
How does the Jedi/Dark Jedi conflict play into the back story of the War, if at all?
(The"Sith", specifically a whole group of original Dark Side counterparts do not exist, with a quasi exception in Palpatine, who's unique in using such abilities without ever being a Jedi)
The nature of Dark Jedi and the power of the Dark Side exist largely in myth, or so it seems. The Jedi have not dealt with those who have turned for hundreds of years, and not dealt with powerful ones for even longer. The dangers of the Dark Side are taught, but not with the same sense of urgency and warning as in the OT. The greater worry with Jedi is simply getting caught up in the petty politics of the Republic, but a looming issue is the strength of their connection with the living Force. Being too involved with non-Jedi matters appears to be a more obvious worry than being turned. Anakin himself has a somewhat limited understanding of the true dangers of the Dark Side.
How does the Galaxy allow for a Dark Jedi/Palpatine to be left in charge of the Empire when all is said and done?
The Republic was simply completely unprepared for a user of the Dark Side like Palpatine to exist. Almost all of those who were sensitive to the Force were either Jedi, half-hearted wielders lacking training(and thus power), or were simply unaware people who didn't understand what they had. None of the Jedi expected a user of the dark side to be as educated and powerful as Palpatine was, especially given that Anakin was the only one of them who ever really spent any time with him and someone who most (Skywalker and possibly Yoda aside) dismissed as a weak President of the Senate who seemed to cater to popular demands.
How many Jedi are we talking about here? A handful like the OT? Two-three handfuls like the GPT? Or a lot a lot?
There are at least a dozen or so Jedi for each populated system. They begin to lose their numbers a bit during the conflict, but largely because a great deal of training is suspended or slowed down during the Clone Wars. The Emperor wipes most of them out towards the end of the war.
How many Dark Jedi?
None, except for Palpatine and eventually Anakin.
What kind of powers do the Force Users have beyond those seen in the OT?
Much of the powers of the Jedi are based on intuition and sense rather than the superpower like nature seen in Lucas' prequels. Being able to realize the amount of ships before sensors do, predict enemy movements, and more heightened detection with the senses. Occasional telekinesis, but much more focus on mental rather than physical befitting the status of those serving as commanders rather than direct soldiers.
What is the Galaxy's general response to Jedi? Are they all assumed to be heroes? Or are people more like Han where they think that it's all religious nonsense?
The Jedi have a mixed reputation in the galaxy. While some praise them as defenders of the Republic, many also show considerable skepticism towards their ways, primarily because they often act independent of the Senate and are remarkably covert and secretive. The vast majority of those in the Republic have never seen a Jedi, let alone how they use their abilities. This isolated nature of them later is shown as mistake by Yoda, who laments that the Jedi lost their connection to the living Force, and by extension, the Republic.
How do your Jedi dress?
There are varieties. Visually, the lower ranked Jedi wear more elaborate clothes, with visual inspiration from both ancient Samurai and Templar Knights. The Jedi Masters wear more simplistic attire, with Yoda in dark green, Obi-Wan in navy blue/black and Anakin in white/light tan.
How organized are the Jedi? Are they like a police force in space or are they more like wizards that are off doing their own thing and maybe have some form or correspondance or a council every now and then? Or something less than that?
The Jedi exist more as a in independent group of religious samurais, serving largely as diplomats and peacebuilders, only acting as soldiers/knights as a last resort. High ranking Jedi communicate with the Senate and system leaders, with decisions made largely internally amongst them. Even on individual planets and stations, the Jedi generally stay isolated, occasionally interacting when necessary. When the war finally occurs, the Jedi serve more as generals and commanders.
Where does the Empire come from?
The Empire emerges in many ways as a result of the frustration of the people in the Republic. The lack of law enforcement in the Outer Rim territories and growing sense of separation between the average citizen and those in the Senate creates great disenchantment throughout the galaxy. Once Palpatine is made President he manages to be so inoffensive to the various factions in the Senate that he ends up with no real enemies, and no real allies.
However, Palpatine's position as President does place him in charge of specific funding for the war, and through various secret investments and machinations, a majority of the Republic army ends up being loyal to him and his associates. At the end of the third film, with the Clone Wars over, and with military control at his side, Palpatine is easily able to transform the Republic and declare himself Emperor, pledging that they will never be invaded by any foreign force again, and claiming that he will still value the input of the Senate. Many citizens support this transformation.
How do the droids fit in to your new story, if at all?
Artoo and Threepio make a quick cameo in each film, with a running gag of the two seemingly about to be involved with the main characters, but never do as they get caught up in their own adventures. They're nice bits of comic relief to provide some lighthearted moments in the midst of the drama.
How is Anakin seduced by the Dark Side? What convinces him to serve the Emperor, the Empire and the Dark Side for 20+ years before allowing Luke to show him the error of his ways.
The continual trauma and losses of the war take a major toll on Anakin as time goes by. As he loses friends and companions to the conflict he grows more and more cynical of the nature of the Republic and of the power of the Jedi. As he and Ben begin to grow apart a bit, his wife and future child become the lynch pin of what optimism and hopes he still has left. When he believes he's lost them, the compassion and idealism of Anakin Skywalker turn into the cynicism and ruthless efficiency of Darth Vader. His faith in everything shattered, the quicker and easier path of the Dark Side offered by the Emperor, one that can get him the results the light sight could not, becomes too tempting to resist. He will have peace and order in the galaxy at any cost. Only when seeing the genuine faith, idealism, and love of his son, does he realize that there is and always was another way.
Who is the main protagonist in your films?
Anakin serves as the main protagonist, with the story starting and ending with with his point of view. Obi-Wan however is the Han Solo-esque deuteragonist, and is the second most important character in the films. When he and Anakin are split, he gets a large focus. Both characters change throughout the movies, though ultimately Skywalker drives more of the plot than Kenobi.