If that's the case, then it is just swapping one giant problem for another. The problem with Episode I is that it drags on and on, doesn't have a solid story, doesn't answer most of the questions it sets up, and works better as "Episode IV" (which is what it really was) than "Episode I".
The SIMPLER we make it, the better.
No Sidious
That's the idea that made me realize Episode I could be saved. No Sidious makes Nute Gunray the "Governor Tarkin" of Episode I. He has a goal -- conquer Amidala. He pursues it and the Jedi oppose him. Their efforts take them through Tatooine, over to Coruscant and back to Naboo. All they want to do is defeat the Trade Federation -- and they hit a lot of opposition, from a droid army, a sith Lord, a beuraucratic senate, a disapproving Jedi council, even an angry bunch of Gungans. But keeping the goal of the story clearly locked between Nute and Amidala gives this movie the potential to have a STORY.
Adding Sidious, Dukoo, General Jar Jar, an unrelated Anakin subplot that never reconnects, a "hunt down the Vergence" agenda, or anything else that cannot be sewn up by the end of this movie will leave us right where GL was -- with mushy structure that does not hold up on repeated viewings.
But if we keep the plot located around the Nute/Amidala conflict, and keep the emotion located around the Qui Gonn/Anakin relationship -- and give both conclusive pay-offs -- then we'll actually have a story.
So I'm agin anything complicated. Dukoo could indeed use some set-up, but TM is handling that over in SOTD and I'm for sacrificing Dukoo material in the interest of better structure in Episode I.