Actually, due to the PT, Stormtroopers are now a mix of clones and non-clones. Not all the clones are from the Jango template.
(Beware of potential spoilers)
Otherwise, I like your ideas. I remember reading the Star Wars novelization as a kid and I always got the impression that Obi Wan was fighting against the clones. I didn't mind how GL actually did it, Order 66 was one of the best and most tragic moments in all of the saga, but the Jedi fighting clones would've been more exciting than them chopping down droids-wiseacre droids at that.
As for Quinlan Vos, I'm a big fan. I hope they don't screw him over in CW S3, but it's cool that they are bringing him aboard.