I'm also praying for the release of 1 & 2 in chronolgical order (The Complete Epic, The Godfather Saga, et al) to be released on DVD.
So are just about all of us on this board.
I guess it's sacreligious to admit that on this website, & I'm sure I'll be ripped apart for it, but I can tell you that most of the people that I've met who worked on the film prefer it that way. The movie flows better &, with all of the extra scenes added back in (Genco dying in the hospital,etc.), it really ties everything together.
The issue of whether the theatrical releases or the chronological version is better has been debated here often. My guess is that posters have been about evenly divided. I prefer the chronological version w/deleted scenes added for the same reasons you cited.