Okay, and here are the actual ideas in no particular order. (How many posts will I keep claiming have ideas when they infact have none?)
1. Setting. The Clone Wars, with an emphasis on WARs. Ash, I came to the same Clone War I and II conclusion you came to but from a slightly different angle. Mostly from a single line from Luke, "You fought in the Clone Wars!?!?" It seemed to him like World War II was to Americans at the time. Not so much Korea or 'Nam. But it seems to me, and I postulated some of this in my General SW Chat thread: http://originaltrilogy.com/forum/topic.cfm/Space-War-Mechanics/topic/10621/ that the more technology is involved, the shorter the warfare. There are no 100s years conflicts in our modern theatre of war like there used to be. War seems to be about comparing forces. When their force is gone and yours is still standing, then you win. It's easier to compare technology so the more of it is involved the faster you find out who has the stronger force and the sooner the conflict comes to its end. At any rate, it's hard for me to imagine a single war to stretch out for many years in the Star Wars Universe. The reason the Rebellion lasts as long as it does is because they are also hiding from the Empire so that they can't simply be wiped out. If you had a War between two or so equal armies that weren't in hiding... seems like one side or the other would win pretty quickly. Therefore, there had to be multiple Clone War's for them to have had a combined length sufficient to leave them in the collective culture for Luke to cry out, "You fought in the Clone Wars!?!?"
When you think of it, a trio of movies known as Star Wars showed very little War. The main trio or quad of A New Hope aren't soldiers or even officially aligned with one side or the other. Leia is, I guess, and she sends the call to adventure to Luke and he picks up the rest of the cast. They're Rebels by the end, but the story by and large is not of the War but by a few people caught in the middle of the War. It might as well have been called "How I Spent My Space Summer (and blew up the death star) by Luke Skywalker" as "Star Wars." So, this is either an argument for or against what I'm about to say next: The main characters of the NPT (I usually call it the MPT for Mulligan Prequel Trilogy) should be soldiers in the armies of the Republic. What they're actually fighting about, how the Clones play into this and all of that I can't seem to figure out... just that the Clone Wars should be portrayed as outright war between at least two large factions.
Which brings me to my next point:
The Republic has no armies and navies of its own. I would compare it to the Allies in World War II or to some degree the United Nations. The Republic is a republic of worlds and is a minimalistic government. To jump to the chase, one of the consequences of the Clone Wars is that the Republic model is considered to be insufficient to keep peace in the Galaxy (too much freedom for bad guys) and the Empire grows out of this. Also, I think the "price" and "damages" of the Clone Wars has to be so high that people would be ready for a more controlling government if it could promise peace.
Which brings me to my next point:
Anakin is a pilot in the Navy of Planet Y. He and Captain (or Sergeant) Obi-Wan Kenobi of Planet Z meet when their respective militaries join forces on Planet X.
Which brings me to my next point:
Jedi Knight Obi-Wan Kenobi is both a Jedi and an officer in the Army. Just like Luke is on Dagobah. Being a Jedi means doing your real job 9-5 and doing Jedi stuff on evenings and weekends maybe other special occasions. I know the analogy isn't the best, but it's something like being a member of a Lodge or a Freemason or something.
2. Alderaan has to be a major player in the story. It's somewhere in the line "General Kenobi served my father in the Clone Wars" and the fact that Leia is handed off to Bail to raise as his daughter. Like a lot of you, that tells me that Notpadme has some strong Alderaanian connection, but what it is exactly I haven't nailed down.
Also, and it heightens the emotion when you see it blowed up good in A New Hope. This is the kind of "casting shadows onto the OT" that I think could be done well on in the NPT.
I still have more ideas, but I've run out of time to get them down here. I promise I'll get back to this in the next day or two or three.