In regards to the OP.
I've always thought the flaws in the PT are flaws in execution, not idea. I think the PTs have fine plots, just poorly pulled off. Even Jar Jar wouldn't be so bad if he'd been pulled off with a little more heart (the Phantom Editor goes a long way towards making Jar Jar into an almost likeable character in The Phantom Edit).
So I guess I'd keep most of it, just have the whole thing re-envisioned to annoy the excesses of style and rework the dramatic moments to actually work.