I finally finished this series. I was not entirely sure I should. Around about episode 15, the narrative became unhinged, and only occasionally got back on track.
When I was a kid, one of the shows I really enjoyed was The Prisoner, starring Patrick McGoohan as a secret agent who has resigned only to discover that secret agents don't retire, they disappear. It was a unique, quirky series, but toward the end it became so quirky that even my then-plastic mind wondered if they had any idea where they were going. Ergo Proxy was guilty of this same derangement, only they started when they were only sixty percent done.
Now I've finished the final episode, and while it involved a lot of lecturing the audience, it tied up the loose threads, and even made some of the nuttier episodes harmonize with the whole. I could still have done without a few of the more dilatory intervals, but I'm mostly satisfied right now.
In the end, it's not up to the grade of better shows I've watched, like Ghost in the Shell: Standalone Complex (way, way better) or Speed Grapher (second tier, but still tons better).