Well, almost everyone will say "get rid of Jar Jar." But besides that, here's one thing I would do different: clone Anakin Skywalker and name that clone Darth Vader.

What this would do is place Obi-Wan as the main character as he trains Darth Vader. Anakin would already by a Jedi at this point. There would be a slightly tension between Anakin and Vader as the two progress through the Clone Wars. At the end, Anakin kills his clone and becomes the Darth Vader we all know.

Speaking of which, the Clone Wars would start to change differently as Vader was the only cloned Jedi to survive the cloning process. The Separatists would attempt to make their own cloned Force-sensitives. This would shift the Clone Wars more to Zahn's version as described in the Thrawn Trilogy, the Separatists soon being called the Clone Masters.

That's all I have right. I'm actually working on a story for this idea, but I have no idea if it might turn out to actually be good. Do you think it might work?