It's eerie how often I'm thinking of a new edit idea for these films and find you've arrived there first. Just last night I was thinking about tweaking the dialogue in Red Pill meeting to remove Morpheus's need for another crew to locate the Oracle, and yup, I track down this thread and you're on it already haha.
Watched the clip, and again there's some great ideas at work, and very well implemented for the most part.
There's a ton of thin characters in the sequels that I find under-developed to the point of uselessness, so I enjoy the little pieces of game footage you've inserted that flesh out a couple of them. Niobe's crew have that extra material to mine, so padding her story out is as good a plan as it was for your first go-around. Locke is necessary to the plot overall, but terribly one-dimensional in the films. You've wisely given him a little more substance.
Niobe's material, and the different introduction to Zion are well intergrated. The removed action scene with Seraph is another winner. It's gone and you wouldn't even notice. Nicely done.
My only notes of concern in the footage so far are these two:
-While I like the added piece where the doormen alert the meeting of the Agent's presence (always felt odd to me how everyone disbands off-screen in the film), the subsequent cut into Neo fighting the Agents is a little jarring. It's not bad by any means, but I feel you may have been a little eager to trim in this instance. The entrance of the Agents was pretty good, their near poetic description of Neo is a great re-introduction to his character and abilities, and conveys their nature at the same time. There's also the moment at the very start of the fight where Neo notices they've been upgraded, which goes some way to explain why he's fighting them at all after so readily taking down Smith at the end of the last film. These are important pieces of information in my opinion, and worth retaining. Definitely bias on my part though. I love the action sequence, it's probably the only one in either sequel that is restrained enough not to outstay its welcome.
-The other concern I have is the cut between Niobe at Zion, and Neo entering the Matrix. I know you're tackling a lot of footage to cut this down to a more reasonable length, but this jump felt a little severe. Depending on what footage you're using and where etc, it might be smart to use a little more footage of Morpheus/Link landing the ship and Neo being jacked in, just to ease the viewer in to the location of these characters. It's hard to juggle when you're really familiar with the material, but as I'm a little distanced from it, I did feel a little lost in where people were. You see Morpheus/Trinity/Link looking on, but you're not aware of their presence until that point, even if you know that logically. This may not be such a big deal in the context of the whole film, but worth noting.
Will be keenly following this. Love Matrix edits, and loved your previous version.