I never once considered the idea proposed here -- but I have to say I LOVE IT!!
Yes, it probably will cause continuity problems-- but the mystery of what the Trade Federation is doing and where Darth Maul comes from will vastly improve the FEELING of that story. Being stuck in the Jedi's shoes, not knowing what the hell is going on is EXACTLY how the story should have been told. I can't believe I never saw this before.
What will need to happen is that the Trade Federation will have to appear stronger, more self-reliant, smart and vast. Darth Maul will be their assistant, provided by a secret sponsor (Sidious) whom is only referred to in passing. Then, Qui Gon's funeral will be full of suspense -- "What the hell was that? A Sith? What the F*** is going on!?" Then we pan over to Palpatine... Excellent.
The other issue to address possibly is making Anakin's final space-ship battle connect with the death of Qui Gon-- I wish someone could use editing to make it seem Anakin feels Qui Gon's death and that he CUTS LOOSE with the torpedoes in an act of wrath and fury over this feeling in the Force.
Do these two things and make the aliens talk alien (which will sure help cover the loss of Sidious) and you may have the best Episode I yet!!
Great idea!!