Review Detail

I liked it. You really tightened it up from what I remember of the theatrical versions. It actually made sense to me as well! I agree with most of the points of the other reviews, it's a step up.
You made me appreciate a few things I thought I never could:
Agent Bane - never clearly felt the connection of Neo knowing about Smith and what it would mean for the machine world (not just the human one)
Tied to that is Neo's real world power. You scaled it back to just sight, and it worked really well.

Now for the audio/video quality, it was great. I watched it on Vimeo, so loading hiccups aside, it looked great.

Visual editing was mostly great. A few scenes I remember noticing editing: When Neo saves Trinity as the building falls. This is not just because it was a memorable scene in theatres, but when they land on the roof, the cuts are really quick and hard. Tough to get around that I know, but it was noticeable.
Another spot was when Smith copies himself into the oracle. This scene is very clearly edited, with most of the oracle's lines omitted.
Another spot was when Mifune is opening the gate. It seemed like he didn't really have an intention to open it and it seemed like there was some editing there to make it fit, it just didn't work for me.
Finally, when Neo and Trinity are going to the machine city there is a shot with the explosives around them where you see Neo reaching out, fighting them (using his "force" powers) It's just a split second, but it took me out of the "no Neo-power" mood. Not that critical though.

Audio editing was also mostly great. The stand out scene that sounded all out of sorts was when Neo meets the oracle and seraph the first time. When they are about to leave the audio did some very weird things.

I gave the lowest score to narrative, but I would score the theatrical versions much much lower. I think it's still too long. The beginning 30 minutes are excessive. While an interesting intro, starting with the meeting would work too. There's just a bit much Niobe.
I like the exclusion of Neo fainting and having power, but he is conspicuously absent after the Nebuchadnezzar blows up. It was handled nicely "sorry for taking so long" so we just assume he's been alone thinking. Still awkward but alright.
I was also conflicted about something near the end. When Neo gets to the machines he knows that Smith is taking over the Matrix and offers his assistance. But he didn't know this prior to going. At first I thought that was a big problem, but it is actually a common theme in the movies. Like the Merovingian says, they simply follow orders. Again and again though it works out for them. In a weird way, Agent Bane worked out for Neo too, since he learns that Smith can get into the real world: if human then machine too. And that's his bargaining chip with the machines. So that's a success of the narrative I first thought was a flaw. Just wanted to add that.
Some action sequences are a bit long, but overall you trimmed stuff up really nicely. I would have taken even more from Zion sequences though.
I'm also not sure about the inclusion of some scenes. One is when Smith gets Seraph and the girl. I guess one needs to make sense of why Seraph isn't there when they reach the Oracle. But the presence of so many Smiths might be sufficient: we realize Seraph was copied. Besides, his end is pretty anticlimactic anyway.

I really enjoyed watching this and will recommend it to others. Thanks for making it!