I would however like to see a better shot and possibly a line of dialog if possible for Neo jacking in to the matrix to fight Smith. It just kinda happens, and the shot of Neo is really quick and doesnt show him paticularly clearly. I would possibly re-use the shot of Neo jacking in from Reloaded at 1:40:32 (at least on my dvd player). It's quick but you can see his face. More importanly, maybe you could use the 10 second from Revolutions from 43:36 "There's something wrong with the Matrix" to 43:46 "This can't be good". This footage would be inserted right after the end of the shot with Evil Bane on the table in a coma and lead into the shot of Neo jacking in to the Matrix. That ten seconds of dialouge makes it sound like Smith has overtaken the Matrix so it fits well right before the fight with Agent Smith. You would have to cut the scene with everyone but Neo talking about finding Niobe from 07:14 - 07:38 in your version, but I think it would make more sense and you still have the sceen later when someone says "we found the logos" so it isnt all that necessary.
There is also a really hard cut to Sati after the fight as the matrix rebuildes itself (the shot with the black cat). Actually I just watched it again, it is less of a hard visual cut than a hard audio cut from the music showing the new oracle to a music cue when the shot of the cat walking by begins. Maybe you could just have the shot of the cat start a second later so the music doesnt change that abrubtly.
No real problems in the middle I think you made the Zion fight SOOO much better. After the war I get why you used the rave sceen as it is actually them celebrating victory as opposed to the Reloaded's celebrating that they're all going to die, but it still runs too long for me. Maybe you could fade out the music and image earlier. Just too much dancing. The dancing is at :91 seconds right now, which is pretty long. I'd make it :35 seconds instead.
Finally, when the Hammer picks up Neo from the machine city there is a shot of the ship flying by followed my Neo in a coma. It's and odd shot transition with a noticable music change. I have a possible suggustion. In the Flight of the Osiris from the Animatrix there is a shot from 4:31 in to 4:34 of a ship flying outside on the surface. You cant see any humans so it really looks just like the films. With these extra three seconds of footage you have both an outside establishing shot (which could easily be taken as the outskirts of machine city) as well as a few seconds that you could use to fade the music by inserting it between the end of the existing Hammer fly-by shot to Neo in sick bay in a coma. Just a suggestion. I havent tried it or anything, so who knows if it would work in the end. There's also another Animatrix "ship only" shot from 4:20-4:23, but I'm not sure how useful that one is.
I think thats it. Again really good great effort. I loved the first Matrix and it killed me how bad the trilogy ended up. Your telling of the story works much better and makes a lot more sense. Especially what you cut out, like Neo having powers in the real world. I also enjoy that you relagated Smith to more of a Darth Maul type bad guy that is taking care of earlier in final film. The war is with the machines not Smith. Smith is a bad ass who gets in the way of winning the war, but he is not the war itself like the orginal Revolutions made him out to be.
If you do any more versions please still put up the divx copy. I'm in Los Angeles, so I wont be getting a DVD anytime soon, and my computer and xbox media player has the ability to adjust the audio sync on the fly so it isnt a problem for me. Dont over think your edit too much, it's already better than the original Revolutions. Like most editors you will probably alway find something you want to change forever and ever no matter how many fixes you make. Keep up the good work.