I agree that the lightning is too much to take out, brash. I don't really see a way to make it work with the other material there is. Not unless you want to do a whole lot of rotoscoping and patch it together from the other movies.

As meaningless as it is, I think the Yoda vs Dooku duel is the best we get in AOTC. They put way more thought into that one than in editing the one with Obi-Wan and Anakin. Maybe there is some extra footage on the DVD's that might help to enhance the duel a bit?