I hope you don't mind talking about the ending and everything else publically, because that's what the forum is for! So here goes.. but...
***** SPOILER ALERT! DISCUSSING THE ENDING OF THE EDIT!! *******
****** DO NOT READ IF YOU WANT TO BE SURPRISED!! *******
First of all, I applaud even your ATTEMPT at this edit. It's a far cry from 95% of what we see here, which is just people sticking in deleted scenes. It's a HUGE amount of work to basically have to memorize these two sequels and then figure out how to re-arrange everything in a way that hopefully turns it into a better film... not to mention the technical hurdles in doing so. So, bravo.
One interesting thing that this edit (and the other fan edits) has done is prove that you just can't turn the Matrix sequels into a good movie. This cut is the best of them so far and it STILL can't save them... but this one does make it far less offensive, and watchable.
I'm glad you took out the rave scene, thank god. During the movie I thought this could be moved to the very end as a sort of "celebration" over winning the war, but your ending works far better.
Whatever people think of your ending, one thing is for sure - IT BEATS THE ORIGINAL.
The biggest problem with the "offical" ending is there is nothing unique about it - it's just a normal, hollywood ending. The Matrix always begged for a twisted, weird, twlilight-zone ending, and yours fits the bill. Sure, it might be a little predictable and simple, but IT WORKS.
The movie itself points out that these events have happened before and Neo had "predecessors." In the end, when there is clearly no winner to the war, the whole thing reboots and starts over.
That makes sense in the context of the Matrix universe, and there is even a glimmer of hope that maybe next time the good guys will win - after all, the Architect tells us that THIS Neo is smarter and faster than the others; maybe the next one will truly be "the one."
The only thing I would change is taking out the Oracle saying "sorry kid" at the end; it's a little too comedic for my taste and changes the mood from "mind bending, unexcpected twist" to "cute."
Otherwise, good stuff and I am sure this is the only version of the sequels I will watch in the future.