Joe Pantoliano does play a good guy in The Fugitive.

If I'd written a sequel, I'd have revealed a Matrix-within-a-Matrix plot, whereby those who are unplugged aren't unplugged at all, merely in a different Matrix for those who think they are unplugged. I'd have then had Neo revealed to be not human but a self-aware computer programme originally programmed to think he is human, who decides to destroy the entire Matrix, freeing humanity but obviously sacrificing his own existence in the process, making a much more powerfully tragic love story with Trinity, and saving her (her death in the third film is stupid and pointless, with no dramatic heft at all). The spiritual aspect of the film would be the mystery of Neo's existence in the first place. Was he created by the Matrix, or did some other force place him in there (immaculate conception?) to free humanity?