1. first of all, well done. you did a good job moving things around to make them make sense, things ive never thought of.
2. the Niobe arriving in zion scene, I've already given you an idea about. I forgot to mention why it makes sense...after Neo looks for the Oracle, the next scene originally is Morpheus flying into Zion. It happens too fast and there is no break. with niobe flying in first it will give the impression that some time passed so that Neo could get back to the ship and then get back to zion. besides, you already make niobe and locke the next scene which is the tailend of the ship returning to zion anyway, so it does fit right there.
3. please dont cut up the animatrix. here is the reason. The way it begins, the stripping fight is an easy way to get into the action. i watched the matrix squared where they start right off with the action, and it is too abrupt. there is no time to get into it. I felt like i missed a scene or something...the way the animatrix starts, it is easy and smooth and then BAM!!! there is action. also, this to me, is part of the whole, this is part of the movie that just happened to be done in CGI. as far as Im concerned it's the first 10 minutes of reloaded. lastly, to deal with your concern of it being cgi...number 1, it is really well done, its not like a cartoon like "kid's story". some parts of that are as real if not more real than some cgi scenes from the film, so don't worry about that. its like if you were going to make a rarities bootleg music cdr, you would include all the b-sides you could find, not just the ones that fit best with the other songs...i dont have a number 2...
4. in this scene during the meeting:
"Neo: Who was that?
Wurm: How did you know someone was here?
Corrupt: He gave you this. He said you set him free.
Wurm: Is everything all right, sir?
Neo: The meeting is over, retreat to your exits. Agents are coming.
Corrupt: Agents?
Neo: Go.
Neo: Hiya, fellas.
[agent 1] It's him.
[agent 2] The Anomaly.
[agent 3] Do we proceed?
[agent 2] Yes.
[agent 3] He is still...
[agent 1]...only human.
-----ETM------
[OR PERHAPS A FEW FIGHTING SHOTS LATER]
INT. Meeting Room (Matrix). This is clearly after the scene in Reloaded, because both Trinity and Morpheus are there, but not Neo. Corrupt comes running down the stairs."
it is my opinion that you should cut to the ETM senes after the agents punch the door once or twice...otherwise you are cutting away from the battle and cutting the flow...
5. the scene with the keymaker locked up and talking to merv...it is not important at all to the film, but for the sake of completion, it should be left in...it gives you an idea as to why he is so willing to have the twins try and kill him after he had been his prisoner for so long. you would think he wouldnt want the keymaker hurt, but that is not the case, this at least gives you insight into the fact that he has run out of patience with him...
6. i agree that the 9 hour/ 3 hour scene shold be moved to later in the film like you suggested
7. the ending showing the oracle...maybe show that somehow a few shots before the "only one survivor" then showing bane ending. the reason being that the bane ending is somewhat more dramatic, and the oracle just sitting there is kind of anti-climatic.
otherwise, great job. again, these are just my opinions and i think this is gonna be a great edit and i cant wait to see it.
thanks