I just posted this in the Radical Redux thread, but I think it's relevant to this cut, given that you want to make Phantom into a stand-alone, swashbuckling adventure flick.
How about replacing all the Sidious holograms with Darth Maul holograms? It'd make him into the primary antagonist, allowing you to end the film with his death and the failure of his scheme to conquer Naboo.