Heck, change all the PT movies, they all lack greatly in the story department. Clones are pretty much a cope out if they just serve a shallow purpose. We need to see the seeds planted in anakin that fracture his personality from Ep. I. Those kinds of things take quite a while to grow and we need to see that in anakin. The story has too many political manuverings in it. We didn't fall in love with the O OT because of the political part of the story, we fell in love with it because of the characters and the dynamic between them. The same needed to be with the Prequels.
Make Obi-wan the good father to anakin. And make Palpy the evil father that twist anakin into believing that Obi-wan is the evil father. Something like that would be far more interesting than what is there now.