First of all, I appreciate your humble attitude towards this. Painful it may have been for you, but I see you learned a lot as you went along. I think you did a fantastic job with this. Just imagine what you could do with a full team of hollywood experts at your disposal.
My feedback for you is as follows:
There is very little of what you cut that I missed as the movie progressed. You have a very good eye for what was extraneous. Exceptions are how you removed the other "ones", but left the scene with the architect about the selection process for the new Zion; and Neo asking Trinity to stay out of the Matrix, but leaving Neo and Morpheus's surprise at her being in it. Both somewhat minor, but it jumped out at me.
What bugged me a bit more is what you didn't cut. Three scenes which I have always had issues with. 1) The Oracle talking about "programs mis-behaving". As much as I love her and her character(and wish there was more of her just because of her perfection for the role), this feels like a director taking time to explain something just to make sure that your average stoopid American doesn't get lost. In this case, just a cryptic hint would have worked far better, especially for rewatchability. 2) The orgasmic dessert in the Merovingian's restaurant. Nice effects and all, but I would rather see it in the extras on the DVD. 3) Last is a big one that I generally hate in *all* movies: Neo removing the bullet from Trinity. In all likelihood, it would be this that was the final cause of her death. It *should be* common knowledge that bullets are often left in their victims as removing it could/would cause more damage than leaving it in. Keep in mind that only the last one really get's on my nerves enough to make me cut my palm with a curved blade.
Yes, the Oracle/Smith scene was clumsy. Thinking more about it, I can imagine what a difficult part this would be to work with. I would have just cut less as there is quite a bit of back-story that I feel is good for the story. IIRC, you weren't happy with the outcome either. No worries though, it didn't hurt your edit much overall.
My biggest issue was the sound, again, something I think you struggled with. Only the first third did I notice the sound not being completely sync'd, especially the Seriph/Neo fight through to the Neo/Smith fight. After that it seemed to get better. But the worst part of the sound must just be the encoding. Don't know what settings you settled on(I'm not a ripper, so I can't make suggestions), but either not enough passes or needed VBR(is that possible in Divx?). A LOT of the sound-heavy scenes got that boomy-crunchy degradation. It certainly is something that happens with a lot of single disc encodes, though. Just a price you pay for so much compression, although I've watched a few movies where this effect was much diminished. Maybe in the future for your xvid releases(and these ones will certainly get most of the viewers from D/Ling) you could double the quality and do two discs? This is how my Matrix Trilogy on my computer is, and I wouldn't have it any other way
Sorry I jump in here at the end and give criticisms which can't be changed :\ You've really done a neat thing here and I applaud you for adding to my enjoyment of the series. You re-edited a gigantic major motion picture BY YOURSELF, and it came out 90% awesome *applause*

Thanks again

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To those who got DVD's, could I perhaps get one from you when possible? I would love to copy this and pass it around to my Matrix-geek friends as well as having a copy with good sound. PM me if this would be possible(rather than me stabbing around trying to find you.