TedEH
Cromulent
I already posted my alternative plot thoughts earlier - and I'd even fleshed it out a little more later on in my head, but in short:Legitimate question, btw, if you were directing this I'd love to know what you would have done differently.
Humans think they've won the war until programs realize they can also escape the matrix by taking jacked-in humans hostage (something something "ransomware" analogy). This takes the fight out of the matrix and into the real world, where the solution/climax comes from realizing it's been Matrix-ception the whole time, explaining why the one had powers outside the matrix. Maybe some new protagonist also has "real"-world one powers. Instead of "winning", they sequel-bait with "but what's happening in the REAL real world?!"
Alternatively, I think most people involved knew that making this movie at all was a trap. The best answer would have been not to make the movie at all. Or make a different movie that isn't billed as a direct sequel to the movie but shares it's themes or some element of it's universe or something.