Hey, believe it or not I've already been working on a project like this! I've spent the last little while splitting the prequel trilogy up into a miniseries. Currently my idea has been to have it be a trilogy of mini-series's (is that a word?). My episode structure currently sits like this:
Season 1: The Phantom Menace
Episode I.I: The Gathering Storm (The whole Naboo opening right up till they escape with Amidala)
Episode I.II: Stranded (All of Tatooine including the Pod Race, Darth Maul has been removed for pacing) I've also considered calling this one "The Great Pod Race"
Episode I.III: Change of the Gaurd (Coruscant right up until they land on Naboo and meet with Gungans, setting up for the big finale)
Episode I.IV: The Battle of Naboo (Title explains it all. Removed parade ending as I felt the darker ending set up the next season best)
Season 2: Attack of the Clones
Episode II.I: The Senator's Peril (Starts at beginning of Ep II and runs until Anikan and Obi Wan tell the counsil about the Bounty hunter)
Episode II.II: Discovery on Kamino (Focus' on Kamino and Anikan and Padme' on Naboo. Ends at Jango fight)
Episode II.III: The Journey Home (Focus' on the Death of Anikan's mom and Obi Wan's capture. Ends when Anikan rush's to rescue)
Episode II.IV: Rescue on Geonosis (Starts with Anikan Landing on Geonosis, ends at "begun, the clone wars have")
Episode II.V: The Sith Witch (Clone wars Vol. 1 compressed into 22 min. Removed everything not relating to Anikan)
Season 3: Revenge of the Sith
Episode III.I: Untitled (Clone Wars Animated vol. 2 starts with Greivous intro from vol. 1 and ends at Dooku Greivous training scene)
Episode III.II: Untitled (Clone Wars Animated vol. 2 starts where last left off, ends at end of vol. 2 with Palpitine's capture
Episode III.III: Untitled (Start of EpIII right up maybe were on wrong side scene.)
Episode III.IV: Untitled (Focus on the Fall of the Jedi, haven't selected end for this one)
Episode III.V: Untitled (Rest of EpIII, again, haven't dealt with this one yet.)
At this point Season 1 is about 95% done, Season 2 is about 70% done, and Season 3 is about 30% done. I'll upload the first episode onto Google video in the next day or so as a pilot so you guys can let me know what you think of the structure. I have no plans at all of doing the OT though, so if someone is interested in doing that alongside me let me know!
Also, is your still with me after all that, my old thread was "Prequel Trilogy Sagafied". The thread is basically dead as the project has changed however, I did upload some footage on that thread that is still active which you can find HERE. Its the first 15 min of Season 3 Episode III.III The footage is hopelessly out of date, but it should give you some idea of my editing style and ideas.
Cheers!