Fixing the whole prequel trilogy would mean re-writing and re-shooting the whole thing.
As far as making the best of The Phantom Menace goes, I like seciors' Return of the Sith. I haven't seen the Magnoliafan changes to Jar Jar's voice, but I suspect that if you added the voice change and subtitles to seciors' edit, you'd be very close.
Are there any other fanedits that changed Jar Jar's voice?