While it may be tempting to write a subtle political drama, I think you must first identify your audience. Who is likely to watch a trilogy of movies dedicated to complex political maneuverings? I doubt that children watching the movies in order would be interested, and adults watching them after seeing the originals would be perplexed at the sudden change of tone. After all, the original trilogy painted the political landscape in broad strokes.
I would make the Republic a macrocosm of Anakin's journey. The question then becomes: Does the prequel trilogy show Anakin's descent into the Dark Side? If so, then the Republic should follow. If not, then the prequels should end with Anakin as a hero and the Republic as victorious, at least for the moment. Both should reveal a tragic flaw, one seen later as the source of their inevitable defeat, and it could be a very stunning revelation in Episode 5.
Consider: The Republic is fighting the Clone Empire. Anakin is a soldier in the Republic army, and the Republic is fearful of its own survival. The mercenary planet of Corellia, with its vast fleet of ships and officers, is for sale to the highest bidder, and its leader, Grand Moff Tarkin, demands governorship over vast expanses of the Republic for his allegiance. The Republic refuses on principle, and the Clone Empire buys the services of Corellia instead. Anakin also is tempted with power, but seemingly rejects it. In Episode 4, the Empire has taken over. We are never told if it is the Clone Empire or the Republic turned Empire, and without this information we can assume that the Clone Empire has triumphed, using the clone-like stormtroopers and the services of the Corellian ships and officers. When it is revealed that the Emperor is the chancellor and Anakin is Vader, we see that Anakin stayed true to the Republic, even as it became an empire. In this way the revelation of Episode 5 becomes that much more potent, and is the hinge on which the entire saga turns.
That's the summary of my basic plot, anyway. I may do an entire thread dedicated to it, if anyone would find it interesting.