Lets bring up one of my favorite problems: the clones. And more specifically the mystery surrounding them and how everyone buys the story of Sifo-Dyas without question.

So here’s a question: What if the clones where never ordered for the Republic, but by some fraction involved with the separatist, for example the Trade Federation?
That way no-one needs to question the clones’ existence as we were handed a sensibly cover up story and only Obi-Wan finding them by accident remains a plot conveniency.

Now the core problem with that is why would they end up fighting for the Republic. And the easy answer would be money. Simply subtitle this alien senator that Bail is arguing with, to say something along the lines of paying the Kaminoans double. This change would even be set up by Dexter in the Diner scene:

Obi-Wan: “Depends on what Dex?”
Dex: “On how well your manners are, and how big your pocketbook is.”

Now everything that remains is to cut the prime minister mentioning the Republic and altering Obi-Wan’s holochat with Yoda and Mace to “…at the request of the Trade Federation…”, he mentions them in the message he sent from Geonosis.
On top of that we could subtitle Poggle to condemn the Kaminoans for their betrayal and change Dooku’s line about the Trade Federation’s “battledroids” being combined with the separatists’ to “forces”. He says force at least once during his battle with Yoda.

This change would even justify Lama Su’s line about the clones being superior to droids better than in the theatrical cut, because originally this line only makes sense after the clone wars ensued.
With this change it would be a call back to Episode I, where we saw the droids fail the Trade Federation.