I agree with eros. Too many "cool looking" throwaway villians, like Maul, Count Dooku, and General Grevious. There should of been only one throughout the prequels, and Dooku would of been the best choice.

EDIT:
OK, to answer the question given, as a general outline of what I would think would be better, stick with the prequel story, but no Jar-Jar, no Darth Maul, No Grevious. Dooku takes Maul's place in TPM, but Qui-Gon/Obi-Wan doesn't know its him, maybe he has a disguise. Its "Darth Tyrannus". Dooku appears in AOTC, and at the end, you find out he is Tyrannus. Make him being sith less obvious. Perhaps throw in a red herring character to help the mystery along. Vader in the suit destroys the Jedi, which would move up the Obi-Wan/Vader fight as well. Vader/Palpatine thinks they destroyed Yoda and Obi-Wan, so you don't have the question of why don't they go after the two most powerful Jedi around. Just a general train of thought on it.