I'm surprised to have only now discovered these boards after researching and working for so long on my own prequel rewrite. I've read the posts on this forum, am working my way through other threads, and much of the suggested material is good. Before I front my own stories, I'd like to respond to different posts.
I noticed that some people think Ben a jerk for "lying" to Luke with regard to his father's identity. However, such a POV neglects critical details offered by the OT.
1. OB1's primary goal was to set Luke on the path to good, going so far as to treat the R2 and the Death Star plans as a secondary concern. Had OB1 told Luke that Anakin was Vader, such knowledge would've been a burden and clouded Luke's feelings. Additionally, OB1's death (at the hand of Vader) instilled anger in Luke, forcing him to commit to the Rebel Alliance and the Force.
2. ESB and ROTJ imply that Luke, inclusive to his training, was responsible for discovering Vader's identity. (For example, in ESB, Luke's confrontation with "Vader" in the cave on Dagobah. Luke might have discovered Vader's true identity if he had talked to Vader, instead of acting aggressively by pulling out his lightsaber. And in ROTJ, Yoda said, "Unfortunate that you rushed to face him. That incomplete was your training. Not ready for the burden were you.") Thus, Ben would've cheated Luke had he been straight with him. Perhaps Ben cheated Anakin in such a fashion, and Ben simply applied his lesson-learned to Luke.
Regarding the secrets and plot twists of the OT...
1. I believe the PT should be OB1's story with Anakin portraying a secondary consequence of OB1's recklessness. Luke's arc would thus be in parallel, portraying Vader's redemption as a consequence to Luke achieving Knighthood. OB1's presence in ANH would then serve as a passing of the baton.
2. Personally, I never felt Darth Vader's revelation was a big surprise. I was a kid and saw it from a mile away. In ESB, Vader was searching for Luke Skywalker before the Emperor ordered him to do so. Why did Vader have an obsession with finding Skywalker, yet be slightly dismissive of the Emperor's concern? While it suggested Vader was planning to overthrow the Emperor, a more subtle motivation seemed to be driving Vader. I would be interested to learn how long beforehand Vader knew of Luke's existence.
3. Leia being Luke's sister. Keeping this a secret is easy. The twins don't have to be born by the end of episode III. In fact, the mother could discover at the film's opening that she is pregnant, and everyone just assumes one baby. This makes it easier to include the mother in action sequences, as opposed to necessitating a 9 month pregnant lady running around.
On Yoda's inclusion... The OT suggested that Vader and the Emperor knew of OB1, but not Yoda (Vader: Obi-Wan can no longer help him; Obi-Wan has taught you well; Obi-Wan was wise to hide her from me, now his failure is complete.) I always thought Yoda was purposefully kept a secret. And this would be easy to achieve. For example, as the Republic grew to be imperialistic, Yoda - and perhaps other Jedi - could have abandoned it. By the start of episode I, Yoda would've been absent for so long that most people in the Republic thought him dead. This would also serve OB1 - he could be on a personal mission to restore the Jedi Order, a goal of such magnitude that it serviced his pride as opposed to his ideals. With the Jedi being absent for so long, it would cause them to fall into realm of hokey religions when accounting for the Empire's propaganda.
The script for ROTJ, in a deleted scene, suggested OB1 and Owen were brothers. While I don't mind Owen and Anakin being brothers/friends, I prefer to stay true to L. Kasden's interpretation.
I'm for leaving Tatooine out, but referencing it as Anakin's home planet. Owen, as OB1's brother, could make a remark about Anakin being better off on the outskirts than in the thick of the Republic's decline.
The Clone Wars... I always thought the Clone Wars were proxy wars with Clones fighting Clones.... The Old Republic got involved with an aggressive interventionist policy, which the Jedi opposed for being born of anger, fear, and aggression. The foreign policy would financially bankrupt the Republic. Star Systems within the Republic would attempt to secede and ultimately be the start of the Rebellion.
I've also wondered about the nature of anger, fear, and aggression as it relates to the Dark Side. Anger was the catalyst for Luke's commitment to the ways of the Jedi and to the Rebellion. In a free market, fear checks excessive greed. But anger, fear, and aggression - when acting together - also describe impatience, both Anakin's and Luke's Achilles' heel.