I really enjoyed the Hacked sequels, well done. You wanted to know about technical glitches:
-Extra frame at the end of the council meeting where Naobi volunteers to search for the N (I can't spell it).
-Sped up/skipping/something like that in the staircase fight with the Frenchman's goons, right before they jump off the balcony.
-Extra frame after the closeup of Mafune during a cutaway from the Zion battle (you can see Kid for a split second).
Those were the only technical glitches I could find. If there are more I was not observant enough to catch them.
There were a few transitions I thought could be done better; I'm not a big fan of the white flashes to the next scene, but maybe there was no other way for you to accomplish some of the transitions. Also, I thought the transition from the Reloaded title to the hallway scene could have been better, as the code simply fades to black. I don't know what else you could do with that, but it just seems inconsistent with what we've seen of the Matrix code before. Maybe a cut to black then to the opening scene similar to what you did in Revolutions.
Storywise, I thought you did a great job, particularly Reloaded. Having the hallway scene from M1 open the film was an excellent decision and really ties a lot of stuff together (Like when Neo says "It felt like being back in that hallway." I was confused as to what he was referring to before, but this time I knew exactly what he meant.) It also makes for a far superior nightmare than Neo having Force visions of Trinity's death or whatever. And the ending of Reloaded was perfect! That's totally what they should have done in the real version! It's a shame about the original Oracle actress dying, and all the story complications is caused as well. I think you did the best you could with what you had to work with though.
As for Revolutions, I know you've said it's more of a rough idea of what you'd have liked to see happen, and you've certainly made a stronger film out of it, but if I may make a few suggestions story wise:
The opening through the end of the Smith fight is great. As much as I like Agent Smith (he really was the best part of the sequels), the war is not about him. He is only an obstacle. I think we lose some of the parallelism between Smith and Neo by taking him out so early, but so be it. That's what the official versions are for.
That said, while watching your edit I had assumed you had taken out the Neo coma/train station plot entirely. I was surprised to see it where you put it, after the final battle. It didn't feel right in that spot, to me anyway. However, that got met thinking, what would you say to this order of events?:
-Your opening up until the conclusion of the Smith fight.
-Neo is in coma after fight, no one knows what happened.
-Insert that whole subplot here, and put back in Sati and her family. That was a good bit remenicent of M1.
-Then back to the main plot, with your continuation and ending except it ends with the celebration and then the final Orcale/Architect/Sati scene.
(In this order of events it probably makes more sense to have Neo and Trinity die. I think one of your goals was to NOT kill them off, so that's really up to you).
-Also, giving Neo the Matrix vision outside the Matrix, for just the Bane-Smith fight would be acceptable I think. Otherwise Neo beating him makes no sense. It can be justified as part of the connection Neo and Smith have. And I know you said you couldn't find a suitable sound clip, but a "Yes, it is" by Keanu would really make it official that when he kills Bane that's the end of Smith. The way it is now Smith sounds like an idiot.
So these are just some ideas that came to me while watching your edit. I have no idea whether they would work or not, and I obviously don't know the Matrix backwards and forwards like you do, so I'd be interested in your opinion on them. Once again great edits and thanks for undertaking such a project, it was obviously no easy task.