First of all, the prequels as one fils is a brilliant idia for a few reasons. You can completly work around all of the jar jar and young anikan stuff with out it bieng a structure problem. For the most part I love what was done with the ep1 part of the editing, good text for the crawl (if a bit fast and dodgy). I don't mind so much that Jar Jar "just hangs arounds" because in turms of the Star Wars films, a creature CG or otherwise bieng around or even a member of the party is nothing new so edited well enough, it works. But as much as I like the idea of the two jedis going to the ship and then flighting Darth Maul, I have a problem with the background. Like it or not Maul is standing next under a big stone archway, and no amount of clever cutting will fix that. Also I think it would work if you had them on the planet and leave the amadala parts in, it brakes up the Jedi well enough. Beyond that I've only seen up to most of the ep2 stuff and it looks good. In my opinion, some of the "dumb jokes" should be left in, like for example Anikan getting crap from obi wan about taking so long and he rebudding about finding the right speeder. I think some of that stuff works and I don't believe you can, or should, have star wars eithout some amount of slap stick. Plus I think at the very least it brake up the pacing of the effects, and without something to distract, the film is just one long effect. And to quote Lucas ironiclly: "A special effect without a story is a pretty boring thing."
It short I think the idea is great, in practice it works for the most part but could use a bit more left in for pacing and such. And I think it would be fine to let it stretch out as long as three and a half or so hours. My two cents!
Great job, can't wait to see a second go of it if you do so.