Nice write-up, and I'll buy a lot of what it's selling. The one bit that doesn't completely jive with how I view the series is the bit about Paradigm existing to keep incrementally improving the "tomato crop" of people until they become an exact match of the people from before Paradigm became...whatever it is now. Not that I think it's wrong or anything, but I just can't recall a whole lot of narrative support for it. I've felt for a long time that episode 14, "Roger the Wanderer," contained some of the most important material for piecing everything together. There's a great line Roger has in there: "It feels like I'm behind the times, or maybe it's the other way around." I think that's us getting a glimpse of the "real" Paradigm, before the catastrophe and domes and artificial holographic stage. Maybe that's just me though.
Man, back in the ancient buried days of forums past I wrote what to be like a 5000-word essay on the show, in which I probably said nothing useful whatsoever. I wonder if that still exists anywhere...