i would scrap Niobe, tanks replacement, the architect, the merovingian, and belluccii as well as dull completely pointless characters like the keymaker. Make the sequel take off on the alegory of the cave, see what would happen if he showed everyone the real world, what their reaction would be. Hell some people could ally themselves with the machines to stop him, it would be more inspired by what Cypher decided to do. And it wouldnt be the complete mess that reloaded was.