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1) Did he have a desk anywhere for when things were calm? What name would you see on the plaque? I'm thinking David as his first name. (feel free to correct me if an official name exists.)
2) What if Smith is trapped in his own perspective of the matrix. His programming is something he's aware of and he wants out of the whole mess. He claims it's about ending humanity, but perhaps he really wanted something else. He wanted his own way out, a freedom from the matrix that could only be achieved by gaining entry to Zion's codes. With that, he could skip town, transfer his data, and settle into some corner as harmless bloatware. But like any attempt he makes, it's thwarted and he ends up faced with deletion or allowing the augmented data the One puts into his program to run rampant.
For topical discussions of the Source Mod remake of Half Life: http://www.gamefaqs.com/boards/683833-black-mesa