I actually like your idea for a Prologue very much it may be the only version of the prequels I would be able to stomached at all considering what Lucas did.
I was wondering if you could make Qui-Gon Jin disappear after he is killed by Maul using rotoscoping technique. Maybe in Kenobi's arms ...
...but really I think Qui-gon should disappear. It would match OT and Qui-gon's ghost was supposed to teach Obiwan on tatowine how to do this, right?
This inconsistency has always been probably my biggest gripe against the PT.