These are all really good ideas. A real fresh start!
I like Blackhawk's approach of Episode I as Obi Wan's encounter with Anakin and the whole "idealistic crusade" idea. Anakin should be no younger than 18. Any younger, and he would not believably be called the best pilot in the galaxy. And would Obi Wan really take someone under 18 off to a potential war?
Anakin should be noble but overconfident, and we should like him. He should never have a "I shouldn't have done that" moment.
In general, the Jedi should be like wandering reclusive monks who only turn to violence as a VERY LAST RESORT. Like wise old martial arts masters who can effortlessly kick your butt with a twig when you insist on attacking them. They should be very few and far between, with low visbility. Some people should even doubt whether they exist at all. In the OT, we see Ben living comfortably in a little hut on Tatooine, and Yoda living in a mud igloo on Degobah. Is there any reason to think that the Jedi haven't always lived like this? I think it certainly fits their philosophy.
Reagrding Owen, I don't think he should be Anakin's brother. Maybe Owen could be Anakin's brother-in-law (his wife's brother, more on that below). Owen should not be a native of Tatooine. The results of the new PT should force Owen into relocating to Tatooine to find a new life and start over. Then we can see the tragedy of his demise in Episode IV, when the galactic conflict he hoped to escape revisits him.
How's this for an idea: when we meet Anakin in Episode I, his last name is not Skywalker. Skywalker is the name of his future wife, and on her planet, it's the wife's name that's passed along, not the husband's. When Anakin gets married (maybe in Episode II), he becomes Anakin Skywalker. Eventually in our new PT, his wife will die, and his rage/revenge will send him over to the dark side. When he becomes Darth Vader, it will be because of his desire to start over as a new person, and to forget his "Skywalker" (married) identity. Remember Vader's words: "That name no longer has any meaning to me."
The Clone Wars. There should be more than one clone War. And they should be fought OVER cloning or AGAINST clones, not with clones as the good guys. It just makes no semantic sense for the wars to be named afer the (supposed) good guys.
Already in my head, I have a theme forming for this new PT: the inability to confront evil and destroy it will always come back to bite you.