- Like the comment above, 1:22:22 does need a re-crop, since the oracle is seen. (good job on this, by the way. I like that Smith is again monologuing here, and the oracle simply responds with a casual nod. Very characteristic of both of them, so it doesn't seem out of place). There's also a very small continuity error where the oracle is holding a cup and a cigarette in one shot, and then when it zooms out you can only see her hand holding a cig. This might be fixed simply by cropping the 2nd shot similarly to whatever you do to 1:22:22.
- I disagree with the above comment about removing the Kid/Mifune scene. This scene helps establish Mifune as a character. Removing this gives him less screen time, thus making his final sacrifice to open the gates a lot less meaningful since we're not as aware of who the character is. It also gives Kid some more screentime and shows his resolve to play his part in the war. Both characters are 2 sides of the same coin, except one has the authority and power to do what he must and the other does not but is still willing to try. Besides, Shinichiro Watanabe made me care about him ever since Animatrix came out, so I might be biased, haha.
- I like what you did concerning the problem of "How Neo lost his eyes." but it's not flowing well because of 2 simple things: You can see the bandage across his eyes as he's trespassed, and after the cut, the shot is too cold/too blue to read as if what just happened, happened. The second can be fixed with color grading, surely, but the previous shot would have to be a combination of level adjustments + rotoscoping, which might be out of your skillset, which would be understandable.
- The moment when Neo and Trinity breach the clouds and see the sky, does not last long enough, and I understand why. There's is not a lot of usable footage here since it's mostly character interaction and you can't exactly show Neo since he's bandaged. But for Trinity, it's something she's never seen before, and it feels like a good opportunity to throw in the slow-motion that is so present through-out the movie. As it is now:
The ship emerges from the clouds and is already descending by the time you cut to the next shot, which in my opinion isn't optimal, since the next shot is aiming directly at the sun and doing that also leaves you no more sky footage to prolong this very important moment (it's the first time in several years a human has looked at the real sun).
I'd say have it breach the clouds, ease into a slow-motion so you get the equivalent of the time you have now for that shot, but the ship has only made half it's progress (still pointing up), cut to trinity saying it's beautiful, ship starting to descend and then back to Trinity, as you see the effects of that descent with the shadows starting to cover her face in the cockpit.
I'm not sure if this would work as I envision it, and definitely not without making use of some pixel-motion interpolation (like twixtor), but I feel like it's some deserved emphasis on an important moment.
-Finally, i don't know how I feel about the epilogue montage. I'd do away with it in it's entirety, but it's ofc my preference. Also it sets up a weird romance between Niobe and Morpheus that counters what was already made evident at the beginning of the movie between her and Lock, and has neo wake up somewhere in the Matrix, which is weird since it seems to have been destroyed by the architect. (Green color coding is always matrix throughout the series, and it's especially apparent when you have Neo dressed in black like that)