I really liked the inclusion of the deleted scenes. It made the whole thing feel a little more original and added to the overall feel of the thing. I also like saving the Death Star for the very end, that would have been a sweet little surprise at the end of it all in the theatres. I have to say I was puzzled as to why the Sidious/Mace fight was cut out, but oh well. I also thought there were some scenes that built up the Anakin/Padme relationship that were cut out when they didn't need to be. It felt like they just sort of got together out of no where and the whole thing was a little forced. Would have like to see Boba too.
Like I said though, really cool way to watch the three movies and definitely something I'll be watching again.