Ok, since I kicked off this whole animated prequel thing, let me throw in some of my thoughts here:
1) I agree with those who say this needs to be 100% original. Not even a wink or a nod to the Lucas prequels.
2) IMO the biggest difference you'll see in a our version VS. the Lucas one is the character of Anakin. Look at James Earl Jones' performance as Darth Vader. His Vader is drastically different from Christensen's. Jones portrays him as cool, collected, and calm. He has a very distinct way of speaking; a sophisticated manner that I don't think just a voice changing box would be capable of. Our Anakin must speak and come off in the same way. Not gentlemanly, but with a cocky chivalry. He's a brash character who has one fatal flaw: pride.
3) The first film should almost be a stand alone adventure. If Vader didn't escape, ANH could work as its own movie without any of the sequels. I think our Episode 1 should be very similar. Like all good first chapters, it serves to introduce you to the world and the characters. That's probably one of the things I dislike the most about TPM. The viewer is expected to have seen the OT in order to understand who Jedi are- they even make a joking reference to the Jedi Mind Trick without even explaining what it is! That would NOT be the case with these films.
4) Artoo and Threepio MUST be a part of this saga. Period.
5) While I certainly dislike the Lucas prequels, I don't think all of his ideas should be thrown out the window. There are plenty of story elements that can be borrowed from the Annotated Screenplays and tons of unused designs in the Art of Star Wars books, etc. that should be utilized to make this seem like it was designed back in the 1977-1983 era.
6) As far as animation style goes, I don't think CGI is very practical. However, if we can come up with base character designs, we could easy create at least a short film or trailer using Flash animation. Creating some sort of trailer should probably be the first goal, as a proof of concept. In fact, I've always envisioned this as a sort of "open source" project with lots of alternate elements floating around the internet for anyone to mashup and use. Think of how many new computer arts students are looking for a good project idea? How many of them would love to have their names on a cool, well respected fan project?