I recently rewatched the "Hacked" fan edits of the Matrix sequels from way back when (my brother was curious, and after probably a decade I figured now was the time for a revisit) and while I still enjoyed them, there were even more things that I noticed that should've been addressed differently or just addressed period (since they're vaguely mentioned in passing and nothing comes of it). I had noticed plenty of these things after watching enough fan edits of the sequels back in 2007-2012, which was even more-so than the things I noticed between 2003-2007 when all I had was the theatrical cuts.
I'm not gonna bother listing everything since, even with the fan edits I did decide to keep (I watched well over a dozen but only kept 3, and then a 4th one I saw maybe 7 years ago) since editors can only work with the footage that exists, but here's something that I don't think can be "re-structured" to fit the narrative better and I don't think I've ever heard ANYONE mention before:
At the end of "Reloaded", we now see that Smith has replicated enough of himself that not only discovered back doors, but the machines haven't once said "Hmmm, this program that didn't delete itself after it was told to do so is now going rogue and very quickly putting a SERIOUS dent in our whole operation. We better take care of it". Instead, Neo choosing to take care of Smith and getting peace between the unplugged humans and the machines is the truce that's decided on until the very end of the next movie.
To me, Smith becoming a virus that replicates himself throughout the 2 films is basically the real life modern day equivalent of the current pandemic of the virus that shall not be named if it was killing millions of people a day after only a month of discovery (possibly less). And on top of that, how did Smith get the keys to all those doors. He must've gone to the Merovingian's hideout and replicated everyone there. However, at the beginning of Revolutions, Mero and his wife are enjoying a night at the club like everything is perfectly fine. Even when Trinity and co. go to him to make a deal to get Neo out of the train station/Limbo, he asks for the Oracle's eyes in exchange for freeing Neo (WTF?).
Now, I understand these 2 movies are already beyond bloated with sub plots and side characters, but to me, in a smaller, smarter and more focused narrative, we would've SEEN Smith take over Mero's castle, grab the keys, and begin his rampage. Then we would've had scenes of Smiths replicated themselves all over cities and countries all over the world. People panicking in the streets trying to hide, newcast reports, World Leaders trying to come together to combat this problem, etc... It could've even simply been a quick 2 minute montage, followed by the machines talking to each other and realizing that their cozy way of doing things was about to come to an end VERY soon if they didn't do anything.
After all that, THEN we get to the truce between Neo and the Machines. But no, instead, the story stays focused on both our heroes, their friends, and the humans already freed in Zion. It's amazing how for 2 movies that seem so big, grand, or epic and how expanded the universe gets, it still feels very small in comparison. It's like how after the first act of Terminator 3 and the big epic chase scene, the movie immediately begins to look and feel like a low budget DTV sequel. Even the 3rd act with everything at the military base felt so small and low budget since we never got any scenes of the machines killing everyone at the base and people running for their lives and being murdered in horrific ways (I sometimes honestly forget that T3 is actually rated R) before flying away from the base and begin chaos all over the world. Nope, Connor and co. go from one quiet abandoned airplane bunker to fly to another quiet, abandoned bunker.
Anyway, I don't know if this really adds anything to the topic of discussion here, but i guess what I'm saying underneath all this is that, after seeing over a dozen fan edits, enjoying and keeping 4 of them (3 of which already did what you're doing in regards to combining the 2 films into 1), I really don't think there's anything that can be done to "save" these movies.
In fact, I would say the only one that really gets it "right" (obviously there is no "real" right version/edit), was the newest one I saw 7-8 years ago (can't remember the name) that strips away the sub plots and characters even more than the other edits do and combines the 2 sequels into 1 movie with a runtime of only like 107 minutes WITH credits. By keeping the general overall plot as small and focused as possible, you never have any time to really think about anything else.