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You misunderstand the metaphor. The batteries scene was about the Matrix as a system of control for harnessing human cognitive output - the Matrix is just a proxy for "The Man" in our world. The entire third movie is about control and purpose vs non-determinism and free will.

I really enjoyed this documentary on Philosophy and the Matrix - https://vimeo.com/53000177

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For the first two, I saw the self-transformation that Neo undertook and the eventual self-sacrifice for the good of all as the overarching "christianity" plot.

I must be missing something. I realize the stories share some similarities but the third movie ends with a Hindu prayer to drive the point home: the Matrix is a fairly classic retelling of the story of Gautama (the Buddha). It follows the Hindu tradition of the story but it's definitely Gautama.

no no no. It is all about the flying spaghetti monster. If you look at the sentinels they all look like flying spaghetti monsters. That was the real intent. The flying spaghetti monster is trying to control us, don't listen to it.

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