1. Don’t Make It A “Real” Reboot, But Rather A Continuation
If you think about it, The Force Awakens was a “Star Wars” reboot. It successfully restarted the Star Wars franchise, which majorly suffered as a result of the prequels. It was its own continuation, but yet it “rebooted” interest in the franchise. The same thing could be done for The Matrix. It has almost been 15 years since the last Matrix movie, The Matrix Revolutions. A lot could have happened after the end of that film.
After all, as The Oracle and Sati are talking at the end of the film about Neo’s possible return, she states that she does not know, but she believed. The door’s already open for a possible continuation of the story of the machine/human war. Perhaps it didn’t end with Neo’s sacrifice. Who’s to say that the machines kept their end of the bargain? How are they going to maintain powered without an energy source? Remember, the sky is still black. They might renege on their deal as a means of survival, and so continues the war between humanity and the machines.