I just had an idea and forgive me if it is foolish or has been discussed before (which is possible since I haven't thoroughly gone over all 215 pages of this thread).

What if Qui-Gon and Count Dooku were the same character?

After all, they seemed to both be mavericks, opposing the Jedi council at times. That way The Phantom Menace and the rest of the prequels are more tied together. Also, their combined character may not be a Sith but just leader of the Seperatists (who may be the precursers to the OT Rebel Alliance). The Jedi won't seem like fools for thinking that Dooku/Jinn is not a killer, and we may sympathize with Dooku. Perhaps for Episode III, Anakin and Obi-Wan can later fight when Obi-Wan finds security tapes from the ship showing that Anakin killed an unarmed Dooku. They may have been supposed to arrest and not outright kill him. The scene may conclude with a line by Anakin that Dooku didn't deserve to live because he gave up his allegiance to the Republic.

I don't know. This is just an idea I had. Feel free to dislike it.