With Neo clearly dead at the end of the trilogy, I'm not sure what Keanu Reeves could do in this sequel... Unless it's some kind of prequel?
I came up with a little synopsis in my head of what they could do to fix the films. The Architect could have gone back on his word of freeing them, as he would no longer be needed if the Matrix was ended. Unnecessary programs are marked for deletion. Fearing his demise, he continues the Matrix. Reprograms Neo to be an Agent.
As for the main character, maybe have a new person join the Resistance. Or focus on Morpheus. Or have Smith join them, as he is supposed to be the opposing force to Neo. If you go with the first two, maybe throughout the film/s, they find out that the Oracle was actually another form of control. If those within the Resistance are always looking for The One, they will always believe that their powers are limited and could never rise to the levels of The One.