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...I suspect they are setting up for the following revelation in Revolutions: ALL of Zion is INSIDE the Matrix, and not just a dependency upon it stuck in a "causality loop" (to paraphrase the Merovingian). Recall the scene where Neo suddenly realizes he can stop the squiddies outside the ship (when the Neb. is getting torpedoed). Recall, too, that Smith was able to transform himself into the spy in Zion -- over the phone.

This would mean that no humans are free, and no machines are free (recalling Smith's comment on why he still chases "the One" even though he was "freed" from his system program obligations). Perhaps all will be set "free" at some moment -- the moment of cataclysmic failure of the programming brought about by a cascading "anamoly," and/or the birth of the REAL real world after 7 "discrete integers" or iterations (to paraphrase the "architect")?

Curious. If all the humans in Zion are part of a carefully crafted sub-routine for control, doesn't this mean that Smith is the only truly "unplugged" independent operator capable of exercising "free choice?" If so, isn't he the good guy? Come to think of it, what does Smith really want? He has said he wants to "get out of here" and must gets the codes to destroy Zion -- and eliminate Neo. In other words, he knows that the only way to destroy THE SYSTEM and liberate himself is to end the Human-Matrix slave-based economy, of which Neo has so far been an integral component. Or is Smith supposed to be the "bad" guy because in so doing he will destroy those humans with the intellectual power of free will, but the constrained ABILITY only to think like slaves (that is, "choosing" slavery by accepting the programming sub-consciously, or acting like Neo in always being the superhero, but never knowing "the why" or using the "muscle that really matters")?