Tell a totally different story.
The current rumor about the new Matrix film's storyline is that it will follow the character of Morpheus. There's also a rumor that Michael B. Jordan (Creed) will be playing this character. Whatever happens with The Matrix prequel, reboot or whatever it is, this film can't simply be a retread of what we've already seen. There is no benefit to that for the characters or the franchise. First of all, part of what made The Matrix so awesome was how this fractured reality story seemed to come out of nowhere. That it told a tale we had kinda seen before (but not really), only seemed to bolster its credibility. Truthfully, the other two films in this franchise were not as amazing as they probably should've been. Heck, the third film felt like it was made with leftovers from the other two. Still, enough time has passed that people would be stoked on a new Matrix movie. More to the point, they'd want to see just how far down the rabbit hole this world goes, not simply where it's been.
Bring back the Wachowskis.
At present Lana and Lilly Wachowski are not involved in this new Matrix film. In fact, Keanu Reeves has gone on record as saying that he is up for another turn as Neo (more on that later), however, he would only come back if the Wachowskis came back. The big question is why wouldn't Warner Bros. give them the chance? Who knows? Maybe they offered this project to Lana and Lilly and they turned it down. These are two iconoclastic directors. They might see re-entering the world of The Matrix as a dry heave. However this plays out, these two should be involved in some way. Maybe not as directors or even producers. Perhaps, they could use their particular sensibility and knowledge of the material to be in charge of the story? Maybe they could write the script? It just doesn't seem right to have a new Matrix film on the docket and not have these people involved in some way.